Re: [gmx-users] Error: No such moleculetype Protein

[Tsjerk Wassenaar]

Hi Anirban,

Probably you have a reference to a group 'Protein' in your .mdp file.

Cheers,

Tsjerk

On Thu, Feb 10, 2011 at 12:01 PM, Anirban Ghosh
 wrote:
> Hi,
> I am trying to convert a CG system containing multiple copies of a protein +
> lipid + water + ions to an all-atom system using the special gromacs_reverse
> version command g_fg2cg. However I am getting the error:
> ---
> calling cpp...
> processing topology...
> Generated 4 of the 780 non-bonded parameter combinations
> Cleaning up temporary file grompp9YJMaA
> ---
> Program g_fg2cg, VERSION 3.3.1
> Source code file: ../kernel/toppush.c, line: 1293
> Fatal error:
> No such moleculetype Protein
> -
> I have checked all the include statements and .itp files, but cannot fix the
> issue. Is seems to be very trivial but still exists.
> Any suggestion is welcome.
>
> Thanks,
> Anirban
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] doubts on g_confrms output

[Tsjerk Wassenaar]

Hi,

The error message says the number of atoms in the first frame is not what
was expected. That indicates the reference structure didn't match, which
suggests the pdb file with the fitted structures wasn't used as reference.
Solution: give the fitted structures both as reference (-s) and as
trajectory (-f) with trjconv.

Cheers,

Tsjerk

On Feb 12, 2011 2:19 AM, "Mark Abraham"  wrote:

On 12/02/2011 3:45 AM, Kwee Hong wrote: > > Hi Mark, > > I tried but with
this error: > > Fatal erro...
OK. I don't know why two frames with different numbers of atoms are written.
Maybe g_confrms -one is useful. Or you can chop apart the PDB by hand in a
text editor.

Mark

>  > From: Mark Abraham <
mark.abra...@anu.edu.au> > To: Discussion...

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Re: [gmx-users] doubts on g_confrms output

[Tsjerk Wassenaar]

Hoi :)

Maybe the following lines are useful. First, to extract the first
model from a PDB file:

sed /ENDMDL/q trajectory.pdb > first.pdb

Just for the record, to extract a specific frame # from a PDB file:

sed -ne '{/^MODEL *# /,/ENDMDL/p}' trajectory.pdb > frame-#.pdb (NOTE:
replace # with the number)

Then, to extract the last frame from a PDB file:

sed -ne '/^MODEL/,/^ENDMDL/{/^MODEL/{x;d};H}' -e '${x;p}'
trajectory.pdb > last.pdb

With these lines it  does not matter whether the frames/models have
equal (numbers of) atoms or not.

Hope it helps,

Tsjerk

On Sat, Feb 12, 2011 at 10:09 AM, David van der Spoel
 wrote:
> On 2011-02-12 02.19, Mark Abraham wrote:
>>
>> On 12/02/2011 3:45 AM, Kwee Hong wrote:
>>>
>>> Hi Mark,
>>>
>>> I tried but with this error:
>>>
>>> Fatal error:
>>> Number of atoms in pdb frame 0 is 331 instead of 491
>>
>> OK. I don't know why two frames with different numbers of atoms are
>> written. Maybe g_confrms -one is useful. Or you can chop apart the PDB
>> by hand in a text editor.
>>
>> Mark
>>
>>> 
>>> *From:* Mark Abraham 
>>> *To:* Discussion list for GROMACS users 
>>> *Sent:* Saturday, February 12, 2011 0:01:39
>>> *Subject:* Re: [gmx-users] doubts on g_confrms output
>>>
>>> On 12/02/2011 2:55 AM, Kwee Hong wrote:
>>>>
>>>> Hi Tsjerk,
>>>>
>>>> Thanks for the help. I got it.
>>>> But do you have any idea how to solve this in vmd?
>>>
>>> Use trjconv -sep on the .pdb file to split it.
>>>
>>> Mark
>>>
>>>>
>>>> Regards,
>>>> Joyce
>>>>
>>>> 
>>>> *From:* Tsjerk Wassenaar 
>>>> *To:* Discussion list for GROMACS users 
>>>> *Sent:* Saturday, January 22, 2011 15:53:22
>>>> *Subject:* Re: [gmx-users] doubts on g_confrms output
>>>>
>>>> Hi Joyce,
>>>>
>>>> In pymol use 'set all_states'
>>>>
>>>> Cheers,
>>>>
>>>> Tsjerk
>>>>
>>>>> On Jan 22, 2011 8:30 AM, "Kwee Hong" >>>> <mailto:jestan1...@yahoo.com>> wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I was trying to do some analysis following John's "GROMACS tutorial
>>>>> for solvation study of spider toxin peptide".
>>>>> I'm using GROMACS-4.5.3 and my command line for g_confrms is
>>>>>
>>>>> g_confrms -f1 1OMB.pdb -f2 md.gro -o fit_wet.pdb
>>>>>
>
> If e.g. 1OMB.pdb does not have hydrogen and md.gro does, you need to specify
> two index files, pointint to e.g. the C-alpha atoms. Then the fit can be
> done on these and your superposition will be fine.
>
>
>>>>> The program calculated the RMSD sucessfully and fit_wet.pdb was
>>>>> generated. Yet, when i tried to visualise fit_wet.pdb using VMD, the
>>>>> structure is obviously in a mess. And when I tried it out with
>>>>> pymol, I can only visualised one model. Model 2 did not appear. I
>>>>> wonder would it be the pdb format generated by g_confrms is not the
>>>>> standard pdb format and had caused VMD and final failed to read them?
>>>>>
>>>>> Herein, I attached part of the pdb file generated by fit_wet.pdb.
>>>>> Any insight is welcomed.
>>>>>
>>>>> Thanks,
>>>>> Joyce
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> gmx-users mailing list gmx-users@gromacs.org
>>>>> <mailto:gmx-users@gromacs.org>
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>> <mailto:gmx-users-requ...@gromacs.org>.
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>>>>
>>>
>>>
>>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.se    http://folding.bmc.uu.se
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Output of Gromacs Demo

[Tsjerk Wassenaar]

Hi Majid,

Check whether you have writing permissions where you're doing the demo.

Cheers,

Tsjerl

On Feb 13, 2011 6:14 AM, "TJ Mustard"  wrote:

 Majid,


 Can you post the exact executions you did.



ie

grompp ..

mdrun ..



This will help alot.

On February 12, 2011 at 7:29 PM majid hasan  wrote:
> Dear All, > I in...

TJ Mustard
Email: musta...@onid.orst.edu

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Re: Fw: [gmx-users] Output of Gromacs Demo

[Tsjerk Wassenaar]

Hi Majid,

Maybe it's a good idea to find somebody around that can help you get started
with using linux. You should get acquainted with that before trying to use
some specialized software.

Cheers,

Tsjerk

On Feb 13, 2011 6:38 PM, "Justin A. Lemkul"  wrote:

majid hasan wrote: > > I have attached the output of "demo", and "water"
with the message. > I jus...
First of all, conf.gro is not an executable, so trying to execute it isn't
going to do anything.  All of this is a result of the fact that you don't
have permission to write files (at the very least) in this system-wide
directory.

-Justin

> I got same output for other files like topol.top etc. > Thanks, > Majid >
> > > > -...
> Browse Top Cars by "Green Rating" <
> http://autos.yahoo.com/green_center/;_ylc=X3oDMTE4MGw4Z2hlBF9TAzk3MTA3MDc2BHNlYwNtYWlsdGFncwRzbGsDZ3JlZW5jZW50ZXI->
> at Yahoo! Autos' Green Center.
>
> 
> TV dinner still cooling?
> Check out "Tonight's Picks" <
> http://us.rd.yahoo.com/evt=49979/*http://tv.yahoo.com/> on Yahoo! TV.
>
>  --  Justin A. Lemkul Ph.D.
Candidate ICTAS Doctoral Schol...
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Re: [gmx-users] visualizing more than 9999 residues....

[Tsjerk Wassenaar]

Hi Anna,

The 'problem' is the PDB file format. It is a fixed-width format that
does not allow for residue numbers with more than 4 digits. Both VMD
and PyMOL do not have problems reading structures with more residues,
but they will choke if you renumber the residues, giving numbers with
five or more digits. It breaks the file format. It may be a bit
troublesome making selections if you have ambiguous residue
identifiers, but that's the way it is with PDB files. You can try to
be creative with chain identifiers and segment identifiers to give all
residues unique markers.

Cheers,

Tsjerk

On Mon, Feb 14, 2011 at 4:29 PM, Anna Marabotti
 wrote:
> Dear gmx-users,
> I have a system formed by protein+ligand+lipid bilayer that accounts for
> about 10500 residues (56000 atoms). It seems to me that it is not possible
> to visualize correctly such a large system with Pymol or VMD, because it
> seems that the max number of residues that I can manage with both programs
> is exactly . Moreover, it's not only a visualization problem, since I
> also had several problems trying to use Pymol or VMD to create the system in
> which the protein+ligand is correctly oriented with respect to the lipid
> bilayer, to proceed further with g_membed. I had several problems in saving
> the .pdb file (after the th residue, the numbering restarted from 0;
> when I manually corrected this prroblem and re-numbered the file, I opened
> it with VMD and Python and found some aberrant visualization of the water
> molecules exceeding the number of . At last, I decided to remove the
> exceeding waters).
> I know that this is a Gromacs user list, not a Pymol or VMD user list, but
> since it seems to me that these two programs are generally considered as a
> "graphical interface" with respect to Gromacs, I'd like to know how you
> folks manage this problem without removing residues. I searched for some
> hints in the gmx-user list and in Google but I didn't find anything.
> Thank you very much and sorry for this off-topic question.
> Anna Marabotti
>
> __
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science - CNR
> Via Roma, 64
> 83100 Avellino
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> E-mail: amarabo...@isa.cnr.it
> Skype account: annam1972
> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
>
> "When a man with a gun meets a man with a pen, the man with the gun is a
> dead man"
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] R: visualizing more than 9999 residues...

[Tsjerk Wassenaar]

Hi Anna,

I didn't say the PDB format does not allow more than  residues. It
does. But it does not allow numbers higher than . Thus, with more
residues, it will start counting over.

Cheers,

Tsjerk

On Mon, Feb 14, 2011 at 4:52 PM, Anna Marabotti
 wrote:
> Dear Tsjerk,
> thank you very much. I really didn't know that the PDB format does not allow
> more than  residues (in fact, it is the first time I have such a big
> system to manage). I will follow your suggestions trying to solve the
> problem with chain identifiers.
> Many thanks and best regards
> Anna
>
> --
>
> Message: 6
> Date: Mon, 14 Feb 2011 16:43:29 +0100
> From: Tsjerk Wassenaar 
> Subject: Re: [gmx-users] visualizing more than  residues
> To: Discussion list for GROMACS users 
> Message-ID:
>        
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Anna,
>
> The 'problem' is the PDB file format. It is a fixed-width format that
> does not allow for residue numbers with more than 4 digits. Both VMD
> and PyMOL do not have problems reading structures with more residues,
> but they will choke if you renumber the residues, giving numbers with
> five or more digits. It breaks the file format. It may be a bit
> troublesome making selections if you have ambiguous residue
> identifiers, but that's the way it is with PDB files. You can try to
> be creative with chain identifiers and segment identifiers to give all
> residues unique markers.
>
> Cheers,
>
> Tsjerk
>
> On Mon, Feb 14, 2011 at 4:29 PM, Anna Marabotti
>  wrote:
>> Dear gmx-users,
>> I have a system formed by protein+ligand+lipid bilayer that accounts for
>> about 10500 residues (56000 atoms). It seems to me that it is not possible
>> to visualize correctly such a large system with Pymol or VMD, because it
>> seems that the max number of residues that I can manage with both programs
>> is exactly . Moreover, it's not only a visualization problem, since I
>> also had several problems trying to use Pymol or VMD to create the system
> in
>> which the protein+ligand is correctly oriented with respect to the lipid
>> bilayer, to proceed further with g_membed. I had several problems in
> saving
>> the .pdb file (after the th residue, the numbering restarted from 0;
>> when I manually corrected this prroblem and re-numbered the file, I opened
>> it with VMD and Python and found some aberrant visualization of the water
>> molecules exceeding the number of . At last, I decided to remove the
>> exceeding waters).
>> I know that this is a Gromacs user list, not a Pymol or VMD user list, but
>> since it seems to me that these two programs are generally considered as a
>> "graphical interface" with respect to Gromacs, I'd like to know how you
>> folks manage this problem without removing residues. I searched for some
>> hints in the gmx-user list and in Google but I didn't find anything.
>> Thank you very much and sorry for this off-topic question.
>> Anna Marabotti
>>
>> __
>> Anna Marabotti, Ph.D.
>> Laboratory of Bioinformatics and Computational Biology
>> Institute of Food Science - CNR
>> Via Roma, 64
>> 83100 Avellino
>> Phone: +39 0825 299651
>> Fax: +39 0825 781585
>> E-mail: amarabo...@isa.cnr.it
>> Skype account: annam1972
>> Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
>>
>> "When a man with a gun meets a man with a pen, the man with the gun is a
>> dead man"
>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
> --
>
> --
> gmx-users mailing list
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>
> End of gmx-users Digest, Vol 82, Issue 111
> ***

Re: [gmx-users] Whereabouts of NDLP???

[Tsjerk Wassenaar]

Hi Ifat,

It has: http://haddock.chem.uu.nl/Squeeze/

Cheers,

Tsjerk

On Tue, Feb 15, 2011 at 12:46 PM, ifat shub  wrote:
> Hi,
> Was this server ever reestablished?
> Is there a link which I can use to calculate the optimal box?
> Thanks,
> Ifat
>
>
>
>
> Hi Alan,
>
> Unfortunately there have been server problems (severe hacking) in
> Groningen some while ago, and the NDLP server was terminated. But,
> we're right about to reestablish an improved server here in Utrecht.
> This server will be much faster, seconds rather than hours - the
> optimal packing for the GroEL/GroES complex (60k atoms) took somewhere
> around a minute maybe, and will also provide an optimal simulation
> cell for a given ensemble (NMR, ENM, MD). In addition, the principal
> author at the time was not in favour of adding the program to the
> Gromacs suite, and there were some depency issues as well. I don't see
> why the new program should not also become incorporated in Gromacs.
>
> That being said, we still need a bit of time here to wrap things up.
> In the mean time, as long as I'm not run over by requests, you can
> send me a (few) structure(s) off the list, and I'll be happy to
> calculate the packing.
>
> Best,
>
> Tsjerk
>
> On Sat, Mar 15, 2008 at 5:15 AM, Alan Chen 
> wrote:
>> Hi All:
>>
>>  I recently came across  Tsjerk Wassenaar's JCC papers about  a
>>  Near-Densest Lattice Packing
>>  algorithm for choosing the optimal triclinic box for a non-spherical
>>  macromolecule.
>>
>> http://www.informatik.uni-trier.de/~ley/db/indices/a-tree/w/Wassenaar:Tsjerk_A=.html
>>
>>  I have a rather cylindrical  RNA I am studying right now, and I wanted
>>  to try out NDLP only the website referred to by the paper
>>  no longer exists, and I can't find any reference to NDLP on the new
>>  rug.nl homepage nor does google give me any clues. Does
>>  anyone know as to this package's current whereabouts?
>>
>>  Thanks,
>>  Alan Chen
>>
>>
>>  ___
>>  gmx-users mailing list    gmx-users at gromacs.org
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi

[Tsjerk Wassenaar]

Hi Ifat,

I guess this is a jump over the periodic boundaries. You should remove
jumps from the trajectory (-pbc nojump) before running g_mindist -pi.

Cheers,

Tsjerk

On Wed, Feb 16, 2011 at 10:19 AM, ifat shub  wrote:
> Hi,
>
>
>
> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
> if the complex is seeing its next periodic image, so I used the g_mindist
> command with the -pi option. My command line was:
>
> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>
> The output (see below) was stable until ~344ps when there is a  jump in the
> max internal distance (third column) from ~6nm to ~22nm. After the jump the
> numbers are reduced back to ~6nm and remained stable until the run is
> completed at 1ns.
>
> Does anyone know how to explain this jump? Is this a real problem or just a
> visualization artifact? Is there a way to avoid such jumps?
>
>
>
> Here is the mdp file I used:
>
> --run.mdp--
>
> integrator  = md
>
> nsteps  = 100
>
> dt  = 0.001
>
> coulombtype = pme
>
> vdw-type    = cut-off
>
> tcoupl  = Berendsen
>
> tc-grps = protein non-protein
>
> tau-t   = 0.1 0.1
>
> ref-t   = 310 310
>
> nstxout = 100
>
> nstvout = 0
>
> nstxtcout   = 100
>
> nstenergy       = 100
>
> comm_mode     = Linear ; Angular
>
> comm_grps    = Protein
>
> xtc_grps   = Protein
>
> energygrps = Protein
>
> --
>
>
>
> Thanks,
>
> Ifat
>
>
>
> The output:
>
> 343.7   10.813 5.924   16.445 16.445 16.445
>
> 343.8   10.809 5.949   16.445 16.445 16.445
>
> 343.9   10.804 5.959   16.445 16.445 16.445
>
> 344  10.808 5.974   16.445 16.445 16.445
>
> 344.1   0.18 21.982 16.445 16.445 16.445
>
> 344.2   10.778 5.977   16.445 16.445 16.445
>
> 344.3   10.768 5.996   16.445 16.445 16.445
>
> 344.4   10.764 6.016   16.445 16.445 16.445
>
> 344.5   10.722 6.029   16.445 16.445 16.445
>
> 344.6   10.774 6.01 16.445 16.445 16.445
>
> 344.7   0.174   21.984 16.445 16.445 16.445
>
> 344.8   0.176   21.98   16.445 16.445 16.445
>
> 344.9   0.17 22.002 16.445 16.445 16.445
>
> 345  0.173   21.981 16.445 16.445 16.445
>
> 345.1   0.191   21.954 16.445 16.445 16.445
>
> 345.2   0.183   21.958 16.445 16.445 16.445
>
> 345.3   0.181   22.012 16.445 16.445 16.445
>
> 345.4   0.17 22.054 16.445 16.445 16.445
>
> 345.5   0.168   22.054 16.445 16.445 16.445
>
> 345.6   0.189   22.039 16.445 16.445 16.445
>
> 345.7   0.171   22.007 16.445 16.445 16.445
>
> 345.8   0.186   22.031 16.445 16.445 16.445
>
> 345.9   0.171   22.077 16.445 16.445 16.445
>
> 346  0.187   21.99   16.445 16.445 16.445
>
> 346.1   0.173   21.984 16.445 16.445 16.445
>
> 346.2   0.181   22.02   16.445 16.445 16.445
>
> 346.3   10.82   5.984   16.445 16.445 16.445
>
> 346.4   10.81   6.002   16.445 16.445 16.445
>
> 346.5   10.819 6.008   16.445 16.445 16.445
>
> 346.6   10.813 5.996   16.445 16.445 16.445
>
> 346.7   10.781 6.006   16.445 16.445 16.445
>
> 346.8   10.793 6.026   16.445 16.445 16.445
>
> 346.9   10.745 5.985   16.445 16.445 16.445
>
> 347  10.762 5.999   16.445 16.445 16.445
>
> 347.1   10.781 5.984   16.445 16.445 16.445
>
> 347.2   10.784 6.002   16.445 16.445 16.445
>
>
>
>
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] g_rmsf reference structure?

[Tsjerk Wassenaar]

Hi,

The reference is used for fitting. The RMSF is calculated with respect
to the average (fitted) structure, unless you explicitly specify that
deviations from the reference should be used.

Cheers,

Tsjerk

On Wed, Feb 16, 2011 at 7:08 AM, Mark Abraham  wrote:
> On 16/02/2011 3:44 PM, kulleperuma.kulleper...@utoronto.ca wrote:
>>
>> Dear all,
>>
>> I use g_rmsf of Gromacs VERSION 4.0.5 to calculate the RMSF of the C-atoms
>> with reference to the average structure between 5-10 ns of a total of 10 ns
>> simulation as below;
>> g_rmsf  ?f md.xtc  ?s md.tpr ?b 5000 ?e 1 ?o rmsf.xvg
>>
>> My understanding of the RMSF is as follows;
>>
>>  RMSF = sqrt( 1/T ?[(xi(t)-Xi)]^2)
>>
>> where T is the time over which one wants to average, and Xi is the
>> reference position of particle i, which is the time-averaged position of the
>> same particle i.
>> What I am confused is whether g_rmsf takes the reference structure from
>> the structure file (-s), which in my case, the md.tpr and NOT the time
>> averaged position over the specified time?
>
> It does take the reference structure from -s. Whether you actually want the
> RMSF from the non-physical time-averaged structure is up to you. IIRC you
> might be able to get such an average from g_cluster.
>
> Mark
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Re: Periodic Boundary Conditions g_mindist -pi

[Tsjerk Wassenaar]

On Wed, Feb 16, 2011 at 1:00 PM, Mark Abraham  wrote:
> On 16/02/2011 10:30 PM, ifat shub wrote:
>
> Hi Tsjerk,
> Thank you for your reply.
> I am aware of the trajconv option but I wanted to know if there is a way to
> avoid these kind of jumps over the periodic boundaries during the mdrun and
> not post process?
>
> No. mdrun does not know in advance what your visualization requirements are,
> and frankly there are better things to do with expensive compute cluster
> time. Post-processing a small number of frames elsewhere is much better use
> of resources.
>

Or:

No. mdrun takes the internal representation that is most efficient,
and there are better things to do with expensive compute cluster time
than writing out a trajectory without jumps, which might not even be
what you want in the end. :)

Tsjerk

> Mark
>
>
>> message: 4
>> Date: Wed, 16 Feb 2011 11:19:14 +0200
>> From: ifat shub 
>> Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi
>> To: gmx-users@gromacs.org
>> Message-ID:
>>        
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi,
>>
>>
>>
>> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see
>> if the complex is seeing its next periodic image, so I used the g_mindist
>> command with the -pi option. My command line was:
>>
>> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi
>>
>> The output (see below) was stable until ~344ps when there is a  jump in
>> the
>> max internal distance (third column) from ~6nm to ~22nm. After the jump
>> the
>> numbers are reduced back to ~6nm and remained stable until the run is
>> completed at 1ns.
>>
>> Does anyone know how to explain this jump? Is this a real problem or just
>> a
>> visualization artifact? Is there a way to avoid such jumps?
>>
>>
>>
>> Here is the mdp file I used:
>>
>> --run.mdp--
>>
>> integrator      = md
>>
>> nsteps          = 100
>>
>> dt              = 0.001
>>
>> coulombtype     = pme
>>
>> vdw-type        = cut-off
>>
>> tcoupl          = Berendsen
>>
>> tc-grps         = protein non-protein
>>
>> tau-t           = 0.1 0.1
>>
>> ref-t           = 310 310
>>
>> nstxout         = 100
>>
>> nstvout         = 0
>>
>> nstxtcout       = 100
>>
>> nstenergy           = 100
>>
>> comm_mode     = Linear ; Angular
>>
>> comm_grps        = Protein
>>
>> xtc_grps               = Protein
>>
>> energygrps         = Protein
>>
>> --
>>
>>
>>
>> Thanks,
>>
>> Ifat
>>
>>
>>
>> The output:
>>
>> 343.7   10.813 5.924   16.445 16.445 16.445
>>
>> 343.8   10.809 5.949   16.445 16.445 16.445
>>
>> 343.9   10.804 5.959   16.445 16.445 16.445
>>
>> 344      10.808 5.974   16.445 16.445 16.445
>>
>> 344.1   0.18     21.982 16.445 16.445 16.445
>>
>> 344.2   10.778 5.977   16.445 16.445 16.445
>>
>> 344.3   10.768 5.996   16.445 16.445 16.445
>>
>> 344.4   10.764 6.016   16.445 16.445 16.445
>>
>> 344.5   10.722 6.029   16.445 16.445 16.445
>>
>> 344.6   10.774 6.01     16.445 16.445 16.445
>>
>> 344.7   0.174   21.984 16.445 16.445 16.445
>>
>> 344.8   0.176   21.98   16.445 16.445 16.445
>>
>> 344.9   0.17     22.002 16.445 16.445 16.445
>>
>> 345      0.173   21.981 16.445 16.445 16.445
>>
>> 345.1   0.191   21.954 16.445 16.445 16.445
>>
>> 345.2   0.183   21.958 16.445 16.445 16.445
>>
>> 345.3   0.181   22.012 16.445 16.445 16.445
>>
>> 345.4   0.17     22.054 16.445 16.445 16.445
>>
>> 345.5   0.168   22.054 16.445 16.445 16.445
>>
>> 345.6   0.189   22.039 16.445 16.445 16.445
>>
>> 345.7   0.171   22.007 16.445 16.445 16.445
>>
>> 345.8   0.186   22.031 16.445 16.445 16.445
>>
>> 345.9   0.171   22.077 16.445 16.445 16.445
>>
>> 346      0.187   21.99   16.445 16.445 16.445
>>
>> 346.1   0.173   21.984 16.445 16.445 16.445
>>
>> 346.2   0.181   22.02   16.445 16.445 16.445
>>
>> 346.3   10.82   5.984   16.445 16.445 16.445
>>
>> 346.4   10.81   6.002   16.445 16.445 16.445
>>
>> 346.5   10.819 6.008   16.445 16.445 16.445
>>
>> 346.6   10.813 5.996   16.445 16.445 16.445
>>
>> 346.7   10.781 6.006   16.445 16.445 16.445
>>
>> 346.8   10.793 6.026   

Re: [gmx-users] g_covar to calculate correlation of motion

[Tsjerk Wassenaar]

Hi Bipin,

Try using a .gro or .pdb file as reference structure (-s). Only .tpr files
are version specific.

Cheers,

Tsjerk

On Feb 21, 2011 8:05 AM, "bipin singh"  wrote:

Dear GMX users,
I want to calculate the correlated motion between atoms during the md simulation
for that purpose I am using g_covar(the one which is available under
http://www.gromacs.org/Downloads/User_contributions/Other_software)

but it is not compatible with the GROMACS-4.5.3, so please suggest me
the alternative way or does anyone have the modified g_covar for
GROMKACS-4.5.3.

-- 
*
-
Thanks and regards
Bipin Singh
*
*
*


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Re: [gmx-users] Re: gmx-users Digest, Vol 82, Issue 150

[Tsjerk Wassenaar]

Hi Evelyne,

> 1) trjconv  -f trajout_dt2000.xtc -s topol.tpr -pbc mol -o trajout_mol.xtc

The option -pbc mol IIRC relates to the option for the unit cell
representation (-ur). To unbreak molecules using trjconv, you need to
have .tpr file and use the option -pbc whole.

> 2) trjconv  -f trajout_mol.xtc -s topol.tpr -pbc nojump trajout_nojump.xtc
> if I use 1) and 2) the system gets "ripped" apart. The system is no longer a
> box but a flat disk (very funky)

This is because the jumps are removed and over time the lipids diffuse
in the plane. They've diffused quite a bit probably, smearing
themselves out over a disk.

Groetjes,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] g_covar to calculate correlation of motion

[Tsjerk Wassenaar]

Hi Bipin,

The file residuetypes.dat is quite different from aminoacids.dat. You
can paste the following into that file (first line is number of
entries, followed by so many residue names):

49
ABU
ACE 
AIB
ALA
ARG
ARGN
ASN
ASN1
ASP
ASP1
ASPH
CYS
CYS1
CYS2
CYSH
DALA
GLN
GLU
GLUH
GLY
HIS
HIS1
HISA
HISB
HISH
HYP
ILE
LEU
LYS
LYSH
MELEU
MET
MEVAL
NAC
NH2
PHE
PHEH
PHEU
PHL
PRO
SER
THR
TRP
TRPH
TRPU
TYR
TYRH
TYRU
VAL


Groetjes,

Tsjerk

On Mon, Feb 21, 2011 at 8:47 AM, bipin singh  wrote:
> Hi,
> Thanks for your suggestion.
> While running the g_covar it is showing the error that aminoacids.dat is not
> found, so i have copied the residuetypes.dat(which i seems the new modified
> name for aminoacids.dat in current GROMACS version), then it prompts to
> choose the group for least square fit, which is not usual groups(i.e protein
> or C alpha groups etc.).please suggest where i have made mistake.
>
> Choose a group for the least squares fit
> Opening library file aminoacids.dat
> WARNING 2 [file aminoacids.dat, line 1]:
>   File aminoacids.dat is empty
> Group 0 (  System) has 30585 elements
> Group 1 ( GLU) has    47 elements
> Group 2 ( HIS) has    86 elements
> Group 3 ( ASN) has   224 elements
> Group 4 ( PRO) has    56 elements
> Group 5 ( VAL) has   272 elements
> Group 6 ( MET) has    68 elements
> Group 7 ( GLY) has   168 elements
> Group 8 ( ILE) has   190 elements
> Group 9 ( ALA) has   110 elements
> Group    10 ( SER) has   143 elements
> Group    11 ( PHE) has    80 elements
> Group    12 ( LYS) has   242 elements
> Group    13 ( TYR) has   189 elements
> Group    14 ( LEU) has   304 elements
> Group    15 ( GLN) has   102 elements
> Group    16 ( TRP) has    48 elements
> Group    17 ( ARG) has   120 elements
> Group    18 ( ASP) has   108 elements
> Group    19 ( THR) has   141 elements
> Group    20 ( SOL) has 27882 elements
> Group    21 (  CL) has 5 elements
>
>
> On Mon, Feb 21, 2011 at 12:44, Tsjerk Wassenaar  wrote:
>>
>> Hi Bipin,
>>
>> Try using a .gro or .pdb file as reference structure (-s). Only .tpr files
>> are version specific.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Feb 21, 2011 8:05 AM, "bipin singh"  wrote:
>>
>> Dear GMX users,
>>
>> I want to calculate the correlated motion between atoms during the md
>> simulation
>>
>> for that purpose I am using g_covar(the one which is available under
>> http://www.gromacs.org/Downloads/User_contributions/Other_software)
>>
>>
>>
>> but it is not compatible with the GROMACS-4.5.3, so please suggest me the
>> alternative way or does anyone have the modified g_covar for
>> GROMKACS-4.5.3.
>>
>> --
>> -
>> Thanks and regards
>> Bipin Singh
>>
>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
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>
>
>
> --
> -
> Thanks and regards
> Bipin Singh
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] Interatomic distance matrices

[Tsjerk Wassenaar]

Hi Nathan,

g_rmsdist gives full matrices, and in .xpm format for which you'd need
to do more scripting than for your original problem :)
But you might find genrestr useful. It can generate constraints for
all distances in a selection, which means you get a half matrix with
the distances. They're not going to be formatted as a half matrix
though. Maybe take these 15 minutes to script it...

Cheers,

Tsjerk

On Wed, Feb 23, 2011 at 7:47 PM, J. Nathan Scott
 wrote:
> Dear Gromacs users,
>
> I was wondering, is there any utility in Gromacs for calculating and
> saving a triangular matrix of interatomic distances from a trajectory
> frame? The website mailing list search seems to be down, and Google
> has not been of much help. g_rmsdist looks like it *might* be able to
> do this, but from the documentation I can't tell whether or not there
> is a set of switches that would allow one to turn off the
> averaging/rms calculation features and instead generate a single frame
> static distance matrix.
>
> If Gromacs can't do this, can anyone recommend another program that
> could generate such matrices? This would not be hard to code, but time
> savers are always appreciated. :)
>
> Best Wishes,
> Nathan
>
> --
> J. Nathan Scott, Ph.D.
> Postdoctoral Fellow
> Department of Chemistry and Biochemistry
> Montana State University
> --
> gmx-users mailing list    gmx-users@gromacs.org
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] negative steps from tpbconv

[Tsjerk Wassenaar]

Hi Jesper,

Using a .cpt file will also work with the modified .tpr file.
Maybe it is also worth considering using the -maxh option to mdrun,
with nsteps in the .mdp file set to -1 (run infinitely). That avoids
the hassle with extensions.

Cheers,

Tsjerk

2011/2/24 Jesper Sørensen :
> Hi Xavier,
>
>
>
> That worked, thanks… Would it also work if I just gave the old state.cpt
> file to mdrun?
>
>
>
> Jesper
>
>
>
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of XAvier Periole
> Sent: 24. februar 2011 12:19
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] negative steps from tpbconv
>
>
>
>
>
> Hi Jesper,
>
>
>
> This occurs when you ask for a number of steps that exceed the
>
> the size of an integer! I got the same problem recently ...
>
>
>
> The only solution I found was to make a new mdp file where t0
>
> is the old time and asking for the extension you need ... you can
>
> give trr and edr files to grompp so the tpr file is a continuation of
>
> earlier one ...
>
>
>
> XAvier.
>
>
>
> On Feb 24, 2011, at 11:50 AM, Jesper Sørensen wrote:
>
> Hi,
>
>
>
> I am trying to extend the run time in tpr file to include more steps using
> tpbconv…
>
> This has worked well for a while, but now I get two errors…
>
> One is that it writes “now -207466 steps”, which doesn’t make sense –
> why is this number negative…
>
> Also, “You've simulated long enough. Not writing tpr file”
>
>
>
> If I extend the simulation using the –nsteps flag, then it will write the
> tpr file, but still comes up with negative numbers whens starting mdrun with
> the file, which mdrun does not exactly like.
>
>
>
> Output is a s follows:
>
> READING COORDS, VELS AND BOX FROM TRAJECTORY
> ../T305/512DPPC_9728W_305K_625ns.trr...
>
>
>
> trn version: GMX_trn_file (single precision)
>
> Read    trr frame   4166: step 212466 time 53116500.000
>
>
>
> Using frame of step 212466 time 5.31165e+07
>
> Extending remaining runtime of by 625000 ps (now -207466 steps)
>
> You've simulated long enough. Not writing tpr file
>
>
>
> Best regards,
>
> Jesper
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] negative steps from tpbconv

[Tsjerk Wassenaar]

Hi,

The .cpt defines the state, not the number of steps to go for.

Setting nsteps to -1 should work for the new (>4.5 definitely, >4.0
I'm not sure) versions of gromacs. I think it was introduced right
after the -maxh option was.

@Xavier: I added a number of editing options to tpbconv (4.5.1), among
which the possibility to set the number of steps directly (which can
then be set to -1). You can take the source code from
/data_new3/tsjerk/GMX/gromacs-4.5.1-rtc/src/kernel/tpbconv.c

Groetjes,

Tsjerk

On Thu, Feb 24, 2011 at 1:35 PM, XAvier Periole  wrote:
>
> I am not sure the use of cpt would work! I might have tried and
> got a problem since the cpt might define where it is going (nsteps) ...
> to be tried!
>
> @Tsjerk: I have not been able to use the nsteps set to -1 for some
> reason it was telling it had ran enough! Any idea why would that be?
>
> On Feb 24, 2011, at 1:01 PM, Tsjerk Wassenaar wrote:
>
>> Hi Jesper,
>>
>> Using a .cpt file will also work with the modified .tpr file.
>> Maybe it is also worth considering using the -maxh option to mdrun,
>> with nsteps in the .mdp file set to -1 (run infinitely). That avoids
>> the hassle with extensions.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> 2011/2/24 Jesper Sørensen :
>>>
>>> Hi Xavier,
>>>
>>>
>>>
>>> That worked, thanks… Would it also work if I just gave the old state.cpt
>>> file to mdrun?
>>>
>>>
>>>
>>> Jesper
>>>
>>>
>>>
>>> From: gmx-users-boun...@gromacs.org
>>> [mailto:gmx-users-boun...@gromacs.org]
>>> On Behalf Of XAvier Periole
>>> Sent: 24. februar 2011 12:19
>>> To: Discussion list for GROMACS users
>>> Subject: Re: [gmx-users] negative steps from tpbconv
>>>
>>>
>>>
>>>
>>>
>>> Hi Jesper,
>>>
>>>
>>>
>>> This occurs when you ask for a number of steps that exceed the
>>>
>>> the size of an integer! I got the same problem recently ...
>>>
>>>
>>>
>>> The only solution I found was to make a new mdp file where t0
>>>
>>> is the old time and asking for the extension you need ... you can
>>>
>>> give trr and edr files to grompp so the tpr file is a continuation of
>>>
>>> earlier one ...
>>>
>>>
>>>
>>> XAvier.
>>>
>>>
>>>
>>> On Feb 24, 2011, at 11:50 AM, Jesper Sørensen wrote:
>>>
>>> Hi,
>>>
>>>
>>>
>>> I am trying to extend the run time in tpr file to include more steps
>>> using
>>> tpbconv…
>>>
>>> This has worked well for a while, but now I get two errors…
>>>
>>> One is that it writes “now -207466 steps”, which doesn’t make sense –
>>> why is this number negative…
>>>
>>> Also, “You've simulated long enough. Not writing tpr file”
>>>
>>>
>>>
>>> If I extend the simulation using the –nsteps flag, then it will write the
>>> tpr file, but still comes up with negative numbers whens starting mdrun
>>> with
>>> the file, which mdrun does not exactly like.
>>>
>>>
>>>
>>> Output is a s follows:
>>>
>>> READING COORDS, VELS AND BOX FROM TRAJECTORY
>>> ../T305/512DPPC_9728W_305K_625ns.trr...
>>>
>>>
>>>
>>> trn version: GMX_trn_file (single precision)
>>>
>>> Read    trr frame   4166: step 212466 time 53116500.000
>>>
>>>
>>>
>>> Using frame of step 212466 time 5.31165e+07
>>>
>>> Extending remaining runtime of by 625000 ps (now -207466 steps)
>>>
>>> You've simulated long enough. Not writing tpr file
>>>
>>>
>>>
>>> Best regards,
>>>
>>> Jesper
>>>
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>> at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>>
>>>
>>>
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>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>

Re: [gmx-users] trjconv problem

[Tsjerk Wassenaar]

Hi Алексей,

We have no use for your PDB files anyway :) In order not to loose the
phospho from your tyrosine, you want to start out with trjconv -pbc
whole. To obtain what you desire, you probably want to give the
following a good read:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
There are some tips there on the use of trjconv.

Cheers,

Tsjerk



On Tue, Mar 1, 2011 at 10:09 AM, Алексей Раевский  wrote:
> Hi, I want to ask you for help. I've got a trr file after 5 ns
> simulation on the desktop 2 quad. The object is a complex of protein
> and ligand (the itp file for ligand was prepeared by server), in
> adition, I made some changes in rtp, atp, bon.itp databases to obtain
> a phosphorylated tyrosine. When I used a trjconv command to convert
> trr to xtc or to pdb I found that my comlex in the first frame was
> devided between several cells (the result of the standard command).
> So I tried different variants to gather everything in one cell:
>
> 1)trjconv -f sys1md.trr -s sys1md.tpr -o dyrk_ehb1.pdb -sep -n
> sys1em1.ndx -b 1 -e 100 -skip 10 -pbc nojump
>
> 2) trjconv -f sys1md.trr -s sys1md.tpr -o dyrk_ehb2.pdb -sep -n
> sys1em1.ndx -b 1 -e 100 -skip 10 -center -pbc mol -ur compact
>
>
> I've even tried to follow one variant by another. But the results are the 
> same.
> As you see I can loose my ligand or  phosphate from tyrosine. Index
> file, I used in the command, contains a new group "complex", which
> includes atoms of protein without hydrogenes, ligand with hydrogenes.
> I've got a one more result, but I can't find this file. In those case
> I loosed some other aminoacids, but ligand and phosphate are Ok.
>
> Thank you
>
> (P.S. I sent a letter with attached sample pdb files, but moderators
> didn't passed it)
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Vectors in non-cubic box

[Tsjerk Wassenaar]

Hi Afsaneh,

The PBC and the .gro file format are explained in the manual, chapter 3.
The last line of the .gro file has the box stored as

XX YY ZZ XY XZ YX YZ ZX ZY

Cheers,

Tsjerk

On Mar 5, 2011 6:03 AM, "afsaneh maleki"  wrote:

Hi,

I want to create  *.gro file with simulation box size as following:

 3.460467452  0.  0.

 1.730233726 2.9968527222000  0.

 0.   0.  10.00

I used the command:

]editconf –f  *.pdb   –o *.gro   –box  3.46   3.46   10.–c–angle
 90  90  60

 are these commands  proper to create this simulation box size?



 system size :  4.975  2.951  0.084 (nm)

center  :  0.025  0.548  0.966 (nm)

box vectors :  0.000  0.000  0.000 (nm)

box angles  :   0.00   0.00   0.00 (degrees)

box volume  :   0.00   (nm^3)

shift   :  2.570  0.951  4.034 (nm)

new center  :  2.595  1.498  5.000 (nm)

new box vectors :  3.460  3.460 10.000 (nm)

new box angles  :  90.00  90.00  60.00 (degrees)

new box volume  : 103.68   (nm^3)



Also I paste some .gro file

1   NAU   39   1.759   1.647   4.998

1   HAC   41   1.855   1.618   4.993

1   HAB   40   1.686   1.578   5.002

   3.46000   2.99645   10.0   0.0   0.0   1.73000   0.
-0.   -0.0



What is three last values in box vector,0.00 -0.00 -.0 0?


Would one please clear me about these vectors?



3.46000   2.99645   10.0   0.0   0.0   1.73000   0.
-0.   -0.0

xx   yy zz ? ?
xy  ?? ?


I have another question that does  g_hbond has the compatibility with
non-cubic (or parallelpiped) cells?


good luck
Afsaneh


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Re: [gmx-users] Vectors in non-cubic box

[Tsjerk Wassenaar]

Hi Afsaneh,

Sorry for missing out on that one. Yes, all tools properly deal with tric.
cells.

Cheers,

Tsjerk

On Mar 5, 2011 7:24 AM, "afsaneh maleki"  wrote:

Thanks Dear Tsjerk

g_hbond has the compatibility with non-cubic (or parallelpiped) cells?
Best wishes,
Afsaneh

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Re: [gmx-users] Replacing a residue and continuing a simulation run

[Tsjerk Wassenaar]

Hi :)

I'd say that if the changes are small you should be able to get away
with it. You might want to start off the second part of the run with a
smaller time step to relax, though. If the change is from TRP to TRP*,
you only need to have a modified topology, without touching the
coordinates. You do need to set up a new  .tpr file from the the .trr
and the modified topology.

Hope it helps,

Tsjerk

On Tue, Mar 15, 2011 at 10:11 PM, Justin A. Lemkul  wrote:
>
>
> J. Nathan Scott wrote:
>>
>> Hello all,
>>
>> I was wondering, is it possible to replace a residue and then continue
>> a simulation using the new parameters/geometry of the new residue? The
>> reason I ask is that I am interested in performing simulations of
>> proteins with tryptophan in its excited state following a lengthy
>> equilibration with TRP in its ground state. I already have reliable
>> excited state atomic charges for the TRP atoms, and I suppose that I
>> will need to change at least some bonded terms to account for the
>> altered geometry of the excited state.
>>
>> I am still in the middle of reading the information that is out there
>> regarding parameterizing new molecules (since I'm using the CHARMM FF,
>> I've been starting to follow Alexander MacKerell's protocols), but I'm
>> still not quite sure as to how one would practically do this residue
>> replacement in the context of a Gromacs run. Will I need to manually
>> edit my .top file, or is there perhaps another way to update the
>> topology file with the new residue following the ground state
>> equilibration? How about coordinates, will I need to transform the TRP
>> coordinates to the excited state geometry by hand?
>>
>
> You would have to hack the topology.  Coordinates are another matter.  If
> you start making ad hoc changes, then what's the point of a continuation?
> Presumably, if you've designed the residue's topology correctly (including
> both bonded and nonbonded parameters), then the residue will adopt the
> correct geometry on its own.
>
> The complication comes with bonded interactions.  Are you using constraints?
>  If so, then changing bond lengths will cause the constraints to fail at
> step 0 (or very soon thereafter) and the simulation will crash.  You can get
> around this by setting "continuation = no" in the .mdp file, but again I
> wonder what the value of the continuation is.  You'd almost certainly have
> to forgo the use of .cpt files, supplying instead your .trr and .edr files
> to preserve as much of the previous ensemble as possible.  Even if you're
> not using constraints, the simulation may still fail if you're suddenly
> changing bond lengths, angles, etc by anything more than a very small
> amount.
>
>> Perhaps the most important question: is there a better way to do the
>> sort of residue replacement I'm contemplating, or is this something
>> that is just inherently going to be a bit messy?
>>
>
> I can't see any way around topology hacking.  If you need different
> parameters, you need a different topology.  It's going to be a bit messy,
> and I would encourage you to give some serious thought to the potential
> pitfalls I listed above.
>
> -Justin
>
>> Thanks very much for any insight or guidance you can offer!
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] g_rms & g-rmsd

[Tsjerk Wassenaar]

Hi Mohsen. These programs calculate quite different things. Please read
their manpages. Read them better if you already read them once ;)

Cheers,

Tsjerk

On Mar 19, 2011 12:16 PM, "mohsen ramezanpour" 
wrote:

Dear All


I have a trajectory(.xtc) and its corresponding .tpr file:
I used the following commands separately but the results were
different,Why??

g_rms-f   trajectory.xtc-s   structure.tpr-n index.ndx-o
rms.xvg
I choosed   group number 12 (drug in pulling problem) for two choose

g_rmsdist   -f   trajectory.xtc-s   structure.tpr   -o
rmsdist.xvg
I choosed the group number 12

Since I didn't determine the reference for g_rms ,I expect the same
results,because both of them choose the tpr structure as the reference one.
Am I right?

Thanks in advance





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Re: [gmx-users] Simulation of slow folding proteins

[Tsjerk Wassenaar]

Hi Bharat,

In addition to the good comments from Chris, mind that to understand
the molecular nature of experimental observations like yours requires
quite a bit of statistics. With just two cases - wild type and
insertion - there is too much uncertainty to claim that possible
differences you observe between the two in a limited (or even
infinite) stretch of time are linked to the difference in the test
tube. Part of them might, but the answer could well be hid in some
unexpected property that is overwhelmed by a seemingly obvious
difference. You would need to have experimental and simulation data on
a whole series of mutants to be able to regress one to the other, and
hope that the differences manisfest themselves in properties that can
be assessed in simulations on the time scales accessible.

Cheers,

Tsjerk

On Tue, Mar 22, 2011 at 2:02 AM,   wrote:
> Dear Bharat:
>
> I hope that this doesn't impede others giving you advice about how to go
> about doing what you want to do, but here's my two cents for what it's
> worth:
>
> My suggestion is to forget about trying to do that. 3-ns simulations are not
> going to give you equilibrium populations of conformational basins (and
> neither would 3-us simulations, I suspect). Not every question is amenable
> to MD on the currently available timescales.
>
> If you really want to try to do it, I would find out what conformations lead
> to flourescence and see if you get more drift away from those conformations
> in some models with longer loops. But again, I think it's probably going to
> be a waste of time.
>
> Chris.
>
> -- original message --
>
> Hi,
>
> I simulated a protein (GFP) with one of its loop replaced with a longer loop
> . After simulating for some 5 to 10 models with different loop sequences , I
> decided to carry out wet-lab experiments for one model on the basis of
> simulation result. The analysis of simulation was done in the following way
> :-
>
> 1) Comparison of RMSD values of backbone - for both GFP wild type and loop
> replaced (mutated GFP)
> 2) Comparison of RMSF of the residues common to both the proteins.
> 3) Visual Inspection of entry of water into GFP.
>
> The simulation was carried out for 3ns for both the proteins.
>
> After that I did the wet-lab experiment for the modeled structure and I
> found the fluorescence to be 50% of the wild type.
>
> Now I want to investigate the reason for this reduction in fluorescence
> ??... How can this be quantified using MD.
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
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>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] question about g_tcaf

[Tsjerk Wassenaar]

Hi Muhammad,

It's 'just' a fit/proportionality parameter relating the viscosity for a
k-vector to the length of the vector and the viscosity proper (eta0). From
the equation you can work out that the unit is nm^-2.

Hope it helps,

Tsjerk

On Thu, Mar 24, 2011 at 10:27 AM, Alif M Latif  wrote:

> Dear gromacs users and developers,
>
> I have 1 question about the calculation of viscosity using g_tcaf. I got
> the visc_k.xvg file. According to Berk Hess's report, the k values should be
> extrapolated to k=0 to obtain the viscosity. The question is (and I'm sorry
> if this is a silly question), what is "a" in : eta(k) = eta 0 (1-ak^2)
> ?..can someone help? I couldn't find (or missed) it in the paper.
>
> Thank You in advance,
>
> MUHAMMAD ALIF MOHAMMAD LATIF
> Laboratory of Theoretical and Computational Chemistry
> Department of Chemistry
> Faculty of Science
> Universiti Putra Malaysia
> 43400 UPM Serdang, Selangor
> MALAYSIA
>
>
>
> --
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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The Netherlands
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Re: [gmx-users] g_tcaf reference

[Tsjerk Wassenaar]

Hi Florian,

It should be Phys. Rev. E i.s.o. JCP.

Cheers,

Tsjerk

On Thu, Mar 24, 2011 at 12:49 PM, Dommert Florian
 wrote:
> Hello,
>
> g_tcaf gives a reference for the method to calculate \eta. However I can
> not find the Palmer JCP 49 (1994), either in a database nor on the JCP
> page. As I want to use the method, I first have to get an idea about it
> and so I need this article to continue. Has anybody an idea where it is
> and how to get it ?
>
> Cheers,
>
> Flo
>
> --
> Florian Dommert
> Dipl. - Phys.
>
> Institute for Computational Physics
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
>
> EMail: domm...@icp.uni-stuttgart.de
> Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
>
> Tel.: +49 - (0)711 - 68563613
> Fax.: +49 - (0)711 - 68563658
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

[Tsjerk Wassenaar]

Hi Maria,

The CHARMM force field is an all-atom one. That means it does not
require improper dihedrals to maintain chirality. If you have a D-ASP
in your structure file, you can rename it to ASP and just run pdb2gmx.
Mind not to regenerate hydrogens in that case, or make sure to modify
the hydrogen position for the D amino acids afterwards, to set the
proper chirality.

Hope it helps,

Tsjerk

On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic
 wrote:
> Hello List
> I want to change an ASP to a D-ASP. I think it should be possible by simply
> changing 2 improper values around the chiral carbon to their opposite sign.
> Instead of making a brand new residue, I thought I would take the topology
> of an ASP generated by pdb2gmx, and simply change values manually in the
> resulting .itp. However, this is not possible because gromacs wants to read
> the dihedral parameters from the ffbonded.itp file. Is it possible for me to
> explicitly state the parameters for these two dihedrals in my d-asp.itp
> file? This will be the fastest solution to the problem because it precludes
> making a new residue or defining new atoms types and so on. With the CHARMM
> force field, I am not sure how  q0 cq translate to c0 c1 c2 and c3 which we
> are used to for gromos topologies.
> The mailing list search function was down, so I could not explore prior
> messages about this.
> --
> Maria
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

[Tsjerk Wassenaar]

Hi Maria,

The general solution is to copy the entry in the .rtp file, modify the
dihedrals involved, and rename the entry to match the name used in the
coordinate (pdb) file. You may also need to copy the entries in the
.hdb file, as well as the .tdb files if it is a terminal residue.

Hope it helps,

Tsjerk

On Fri, Mar 25, 2011 at 12:12 PM, maria goranovic
 wrote:
> Hi
> Appreciate the quick help
> I am sorry, this is not an improper, but a proper dihedral that holds the
> chirality in place. Then the solution suggested by Meli would not work? I do
> not have a D-ASP. I in fact have an L-ASP which i want to convert to D. So
> the question is simply how to set the proper chirality to a D-amino acid in
> CHARMM.
>
>
> Maria
> On Fri, Mar 25, 2011 at 11:49 AM, Tsjerk Wassenaar 
> wrote:
>>
>> Hi Maria,
>>
>> The CHARMM force field is an all-atom one. That means it does not
>> require improper dihedrals to maintain chirality. If you have a D-ASP
>> in your structure file, you can rename it to ASP and just run pdb2gmx.
>> Mind not to regenerate hydrogens in that case, or make sure to modify
>> the hydrogen position for the D amino acids afterwards, to set the
>> proper chirality.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Fri, Mar 25, 2011 at 11:09 AM, maria goranovic
>>  wrote:
>> > Hello List
>> > I want to change an ASP to a D-ASP. I think it should be possible by
>> > simply
>> > changing 2 improper values around the chiral carbon to their opposite
>> > sign.
>> > Instead of making a brand new residue, I thought I would take the
>> > topology
>> > of an ASP generated by pdb2gmx, and simply change values manually in the
>> > resulting .itp. However, this is not possible because gromacs wants to
>> > read
>> > the dihedral parameters from the ffbonded.itp file. Is it possible for
>> > me to
>> > explicitly state the parameters for these two dihedrals in my d-asp.itp
>> > file? This will be the fastest solution to the problem because it
>> > precludes
>> > making a new residue or defining new atoms types and so on. With the
>> > CHARMM
>> > force field, I am not sure how  q0 cq translate to c0 c1 c2 and c3 which
>> > we
>> > are used to for gromos topologies.
>> > The mailing list search function was down, so I could not explore prior
>> > messages about this.
>> > --
>> > Maria
>> >
>> > --
>> > Maria G.
>> > Technical University of Denmark
>> > Copenhagen
>> >
>> > --
>> > gmx-users mailing list    gmx-users@gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-requ...@gromacs.org.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] RMSD Calculation

[Tsjerk Wassenaar]

Hey :)

You probably want to fit on the protein and calculate the RMSD on the
ligand. You may need to specify these groups in an index file.

Hope it helps,

Tsjerk

On Mar 27, 2011 3:28 AM, "Justin A. Lemkul"  wrote:

Nancy wrote: > > Hi All, > > I need to determine the RMSD of a small
molecule cocrystallized ligan...
I answered this yesterday:

http://lists.gromacs.org/pipermail/gmx-users/2011-March/059697.html

If there's some reason you can't get that to work, then don't simply re-post
the same original question.  Iterative calls to g_rms are quite
straightforward to script.

-Justin

> Thank you very much, > Nancy >
-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] oligoglycines

[Tsjerk Wassenaar]

Hi Nisha,

For building you can also use pymol if you have it installed. On the
command line you can issue:

pymol -qcd 'editor.build_peptide("GGG");cmd.save("triglycine.pdb","not hydro")'

Hope it helps,

Tsjerk

On Mon, Mar 28, 2011 at 6:05 PM,   wrote:
> Hello,
>
>   I want to simulate n-glycines (diglycine, triglycine..etc) I tried to get
> the structure from PRODRG, but the program adds H's on the N-terminal
> instead of on C- terminal. Is there another program I could use, or a site
> where I could get the structure of oligoglycines? For example, diglycine
> (NH2-CH2-CO-NH-CH2-COOH), but PRODRG gives me ((NH3-CH2-CO-NH-CH2-COO)
>
> Thanks!
>
> Nisha P
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Re: Which structure to be used during covariance analysis

[Tsjerk Wassenaar]

Hi Bipin,

That won't really matter. The reference is just for fitting.

Cheers,

Tsjerk

On Mar 29, 2011 3:51 PM, "bipin singh"  wrote:

> > Hello, > I just want to know which structure to be used during
covariance analysis with g_cov...

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Re: [gmx-users] the total charge of system is not an integer

[Tsjerk Wassenaar]

Hi Ahmet,

As suggested, it's better to break up your molecule into smaller
charge groups. Note that charge groups don't need to have zero charge,
nor integer charge. In your case, I'd suggest two COH groups for EDO,
which will have zero net charge each, and for TRS I'd take the COH
groups as separate charge groups. I also note that the COH groups,
although chemically identical - H3NC(COH)3, right?-, have different
charges. That doesn't seem proper.

Hope it helps,

Tsjerk

2011/3/31 ahmet yıldırım :
> Dear users,
>
> Before energy minimization step , I performed the preprosessing step using
> grompp .
> However, there are two note that :
>
> NOTE 1 [file topol.top, line 52]:
>   System has non-zero total charge: -1.50e+01
>
> NOTE 2 [file topol.top]:
>   The largest charge group contains 11 atoms.
>   Since atoms only see each other when the centers of geometry of the charge
>   groups they belong to are within the cut-off distance, too large charge
>   groups can lead to serious cut-off artifacts.
>   For efficiency and accuracy, charge group should consist of a few atoms.
>   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>
> PS: TRS and EDO are not aminoacid
>
> TRS.itp:
> ..
> [ moleculetype ]
> ; Name nrexcl
> TRS  3
>
> [ atoms ]
> ;   nr  type  resnr resid  atom  cgnr   charge mass
>  1    OA 1  TRS  O1 1   -0.119  15.9994
>  2 H 1  TRS H13 1    0.032   1.0080
>  3   CH2 1  TRS  C1 1    0.087  14.0270
>  4  CCl4 1  TRS   C 2    0.055  12.0110
>  5   CH2 1  TRS  C3 2    0.049  14.0270
>  6    OA 1  TRS  O3 2   -0.205  15.9994
>  7 H 1  TRS H33 2    0.019   1.0080
>  8    NL 1  TRS   N 2    0.206  14.0067
>  9 H 1  TRS  H2 2    0.004   1.0080
>     10 H 1  TRS  H3 2    0.004   1.0080
>     11 H 1  TRS  H1 2    0.004   1.0080
>     12   CH2 1  TRS  C2 2    0.050  14.0270
>     13    OA 1  TRS  O2 2   -0.205  15.9994
>     14 H 1  TRS H23 2    0.019   1.0080
> ...
>
> EDO.itp
> ...
> [ moleculetype ]
> ; Name nrexcl
> EDO  3
>
> [ atoms ]
> ;   nr  type  resnr resid  atom  cgnr   charge mass
>  1    OA 1  EDO OAB 1   -0.111  15.9994
>  2 H 1  EDO HAE 1    0.031   1.0080
>  3   CH2 1  EDO CAA 1    0.080  14.0270
>  4   CH2 1  EDO CAC 1    0.080  14.0270
>  5    OA 1  EDO OAD 1   -0.111  15.9994
>  6 H 1  EDO HAF 1    0.031   1.0080
> ...
>
> topol.top:
> ..
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
> #include "TRS.itp"
> #include "EDO.itp"
> ..
> [ molecules ]
> ; Compound    #mols
> Protein_chain_A 1
> Protein_chain_B 1
> SOL   185
> SOL   143
> TRS    1
> EDO    1
> SOL 44125
>
> Conf.gro:
> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
>  5354
>     2GLN  N    1   1.458  -1.158   0.739
>     2GLN H1    2   1.520  -1.083   0.763
> ...
>   485HOH    HW1 5333   0.221  -3.864  -2.291
>   485HOH    HW2 5334   0.303  -3.946  -2.407
>     1TRS  O1   1  -3.812  -0.471  -2.002
>     1TRS  H13  2  -3.865  -0.443  -1.922
>     1TRS  C1   3  -3.672  -0.469  -1.971
>     1TRS  C    4  -3.635  -0.571  -1.863
>     1TRS  C3   5  -3.711  -0.547  -1.731
>     1TRS  O3   6  -3.694  -0.414  -1.679
>     1TRS  H33  7  -3.746  -0.404  -1.594
>     1TRS  N    8  -3.673  -0.705  -1.911
>     1TRS  H2   9  -3.625  -0.725  -1.996
>     1TRS  H3  10  -3.771  -0.707  -1.927
>     1TRS  H1  11  -3.649  -0.774  -1.842
>     1TRS  C2  12  -3.483  -0.573  -1.840
>     1TRS  O2  13  -3.428  -0.445  -1.806
>     1TRS  H23 14  -3.470  -0.412  -1.722
>     1EDO  OAB  1   0.307  -2.792   0.149
>     1EDO  HAE  2   0.390  -2.826   0.104
>     1EDO  CAA  3   0.239  -2.901   0.212
>     1EDO  CAC  4   0.111  -2.851   0.281
>     1EDO  OAD  5   0.144  -2.763   0.388
>     1EDO  HAF  6   0.060  -2.731   0.432
>    8.13100   7.04165  13.54850   0.0   0.0  -4.06550   0.0
> 0.0   0.0
>
> How can I fixed these notes(note 1 and note 2)?
>
> Thanks in advance
> --
> Ahmet YILDIRIM
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular R

Re: [gmx-users] the total charge of system is not an integer

[Tsjerk Wassenaar]

Hi Ahmet,

Why would I get angry? :) Sending a reply to the list will not usually
be taken as asking for private tutoring...

As Mark pointed out, you need to get familiar with the format of the
files. That's the first thing you should do if you get to the point of
needing to use non standard topologies. Read the manual, look at
existing files. As for the immediate question, under the [ atoms ]
section is a line indicating which column denotes what. You'd need to
modify the columns 'cgnr' (charge group number) and probably 'charge'.
For finding proper charge groups, in general you best draw your
molecule, with the charges added, and then see which atoms would
almost naturally group together.

TRS.itp:
..
[ moleculetype ]
; Name nrexcl
TRS  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  TRS  O1 1   -0.119  15.9994
 2 H 1  TRS H13 10.032   1.0080
 3   CH2 1  TRS  C1 10.087  14.0270
 4  CCl4 1  TRS   C 20.055  12.0110
 5   CH2 1  TRS  C3 20.049  14.0270
 6OA 1  TRS  O3 2   -0.205  15.9994

Hope it helps,

Tsjerk



2011/3/31 ahmet yıldırım :
> Dear Tsjerk,
>
> I will ask you one thing but please do not get angry (I know you are not a
> private tutor but I need your helps).
>
> How do I apply on the files (EDO.itp and TRS.itp) that you said? (or can you
> suggest a tutorial?)
>
> Thanks
>
> 2011/3/31 Mark Abraham 
>>
>> On 31/03/2011 5:18 PM, ahmet yıldırım wrote:
>>
>> Dear users,
>>
>> Before energy minimization step , I performed the preprosessing step using
>> grompp .
>> However, there are two note that :
>>
>> NOTE 1 [file topol.top, line 52]:
>>   System has non-zero total charge: -1.50e+01
>>
>> This is an integer. See
>> http://en.wikipedia.org/wiki/Scientific_notation#E_notation and
>> http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>>
>> NOTE 2 [file topol.top]:
>>   The largest charge group contains 11 atoms.
>>   Since atoms only see each other when the centers of geometry of the
>> charge
>>   groups they belong to are within the cut-off distance, too large charge
>>   groups can lead to serious cut-off artifacts.
>>   For efficiency and accuracy, charge group should consist of a few atoms.
>>   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
>>
>> See Tsjerk's email.
>>
>> Mark
>>
>>
>> PS: TRS and EDO are not aminoacid
>>
>> TRS.itp:
>> ..
>> [ moleculetype ]
>> ; Name nrexcl
>> TRS  3
>>
>> [ atoms ]
>> ;   nr  type  resnr resid  atom  cgnr   charge mass
>>  1    OA 1  TRS  O1 1   -0.119  15.9994
>>  2 H 1  TRS H13 1    0.032   1.0080
>>  3   CH2 1  TRS  C1 1    0.087  14.0270
>>  4  CCl4 1  TRS   C 2    0.055  12.0110
>>  5   CH2 1  TRS  C3 2    0.049  14.0270
>>  6    OA 1  TRS  O3 2   -0.205  15.9994
>>  7 H 1  TRS H33 2    0.019   1.0080
>>  8    NL 1  TRS   N 2    0.206  14.0067
>>  9 H 1  TRS  H2 2    0.004   1.0080
>>     10 H 1  TRS  H3 2    0.004   1.0080
>>     11 H 1  TRS  H1 2    0.004   1.0080
>>     12   CH2 1  TRS  C2 2    0.050  14.0270
>>     13    OA 1  TRS  O2 2   -0.205  15.9994
>>     14 H 1  TRS H23 2    0.019   1.0080
>> ...
>>
>> EDO.itp
>> ...
>> [ moleculetype ]
>> ; Name nrexcl
>> EDO  3
>>
>> [ atoms ]
>> ;   nr  type  resnr resid  atom  cgnr   charge mass
>>  1    OA 1  EDO OAB 1   -0.111  15.9994
>>  2 H 1  EDO HAE 1    0.031   1.0080
>>  3   CH2 1  EDO CAA 1    0.080  14.0270
>>  4   CH2 1  EDO CAC 1    0.080  14.0270
>>  5    OA 1  EDO OAD 1   -0.111  15.9994
>>  6 H 1  EDO HAF 1    0.031   1.0080
>> ...
>>
>> topol.top:
>> ..
>> ; Include water topology
>> #include "gromos43a1.ff/spc.itp"
>> #include "TRS.itp"
>> #include "EDO.itp"
>> ..
>> [ molecules ]
>> ; Compound    #mols
>> Protein_chain_A 1
>> Protein_chain_B 1
>> SOL   185
>> SOL   143
>> TRS    1
>> EDO    1
>> SOL 44125
>>
>> Conf.gro:
>> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
>>  5354
>>     2GLN  N    1   1.458  -1.158   0.739
>>     2GLN H1    2   1.520  -1.083   0.763
>> ...
>>   485HOH    HW1 5333   0.221  -3.864  -2.291
>>   485HOH    HW2 5334   0.303  -3.946  -2.407
>>     1TRS  O1   1  -3.812  -0.471  -2.002
>>     1TRS  H13  2  -3.865  -0.443  -1.922
>>     1TRS  C1   3  -3.672  -0.469  -1.971
>>     1TRS  C    4  -3.635  -0.571  -1.863
>>     1TRS  C3   5  -3.711  -0.547  -1.731
>>     1TRS  O3   6  -3.694  -0.414  -1.679
>>     1TRS  

Re: [gmx-users] adding a new residue in the ff

[Tsjerk Wassenaar]

Hi,

> It would probably be easier, faster, and more accurate to just use most of
> the parameters for Cys rather than try to have PRODRG re-create a
> (potentially flawed) model of your compound.  The only new parameters are
> related to SO3, so the rest should be identical to the Cys residue.

That's not a good idea. It'll only do for the backbone. The charge of
CB will be quite different, as well as the CA-CB-SG angle, and for the
rest there's nothing similar even.

> This is where parameterization becomes a chore - when there's nothing
> analogous to what you're doing.  Proper Gromos96 parameterization
> methodology would dictate that you generate an analogous compound (i.e.,
> methyl sulfonic acid) and adjust its parameters such that it reproduces
> various condensed-phase thermodynamic and physical properties (DeltaG of
> solvation, liquid density, heat of vaporization).  Proper derivation is
> quite time-consuming.  Perhaps someone has already done this work and it is
> published.  If you're unlucky, you've got to do it all yourself.

That's a good idea :)

Cheers,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] FW: protein split over boundary

[Tsjerk Wassenaar]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-TAW

On Fri, Apr 1, 2011 at 10:53 AM, anahita  wrote:
>
>
>
>
> From: anahita [mailto:ana_j0...@yahoo.com]
> Sent: Friday, April 01, 2011 1:13 PM
> To: 'gmx-users-requ...@gromacs.org'
> Subject: protein split over boundary
>
>
>
> Dear user,
>
> Hello, I appreciate if somebody help me. During the simulation of my protein
> I didn’t get any error but after 1ns of MD
>
> my molecule was split over boundary in cubic box. it means some part of it
> enter the other side of the box.
>
> At first,For decreasing the cost of simulation, in “editconf” command I set
> the number “d” on 0.9  to decease the box size. I want to mention that
> during the calculation my rvdw is 1.4.
>
> I want to know instead of problem of visualization, the other things is
> fine?
>
> Best regards.
>
> A. johari
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] how to simulate crystals in Gromacs

[Tsjerk Wassenaar]

Hi,

When building crystals, you first have to generate all symmetry mates
for a single unit cell. This may involve both rotations and
translations, and the information should be present in the structure
file. The unit cell can then be used to build a larger crystal with
genconf. With Pymol you can build symmetry mates from a structure
file, and on the pymolwiki there's a script to build a unit cell for a
given structure.
Mind first to convert the structure into the proper format for the
force field description you're using, as it will be more convenient to
build the topology for the crystal afterwards.

Hope it helps,

Tsjerk

2011/4/7 Mark Abraham :
> On 7/04/2011 4:21 PM, ZHANG Lu wrote:
>> Thank you for your answer.
>> Could you give me some advice on the size of cell box? What is the proper
>> size if I want to do MD simulation in crystal environment?
>> I didn't change the cell size when I convert cif file to pdb file; in
>> other word, I didn't use editconf to produce the cell box. What I did was
>> just :
>> pdb2gmx -> genconf ( -nbox 10 10 10 -dist 0.5 0.5 0.5 ) -> genbox. Was it
>> wrong?
>
> I don't know. When you opened it in a visualization program and saw the
> periodic box, and turned on the "show periodic images" option, did it
> look reasonable?
>
> Mark
>
>> Below is the coordination and cell box after I run pdb2gmx. I use water to
>> fill in the box after genconf.
>>
>>     1CLC    OBD    1  -0.042   0.476   0.219
>>     1CLC    O1D    2  -0.298   0.731   0.310
>>     1CLC    O2D    3  -0.163   0.650   0.469
>>     1CLC    O1A    4  -0.697   0.691   0.093
>>     1CLC    O2A    5  -0.822   0.826   0.214
>>     1CLC    CMB    6  -0.877   0.164   0.937
>>     1CLC    CAB    7  -0.708  -0.089   1.050
>>     1CLC    CBB    8  -0.820  -0.108   1.104
>>     1CLC    CMC    9  -0.224  -0.302   0.948
>>     1CLC    CAC   10   0.016  -0.236   0.743
>>     1CLC    CBC   11   0.014  -0.333   0.627
>>     1CLC    CMD   12   0.106   0.164   0.377
>>     1CLC    CAD   13  -0.122   0.426   0.298
>>     1CLC    CBD   14  -0.260   0.494   0.322
>>     1CLC    CAA   15  -0.598   0.558   0.332
>>     1CLC    CBA   16  -0.685   0.684   0.330
>>     1CLC    CMA   17  -0.672   0.604   0.686
>>     1CLC    CGD   18  -0.246   0.640   0.366
>>     1CLC    CED   19  -0.149   0.789   0.509
>>     1CLC    CGA   20  -0.733   0.732   0.198
>>     1CLC     C1   21  -0.878   0.885   0.095
>>     1CLC    CMG   22  -0.373   0.175   0.683
>>     1CLC     NB   23  -0.540   0.110   0.783
>>     1CLC     NC   24  -0.278  -0.005   0.729
>>     1CLC     ND   25  -0.234   0.194   0.534
>>     1CLC     NA   26  -0.492   0.328   0.583
>>     1CLC    C1B   27  -0.657   0.181   0.798
>>     1CLC    C2B   28  -0.741   0.114   0.897
>>     1CLC    C3B   29  -0.670   0.008   0.944
>>     1CLC    C4B   30  -0.543   0.006   0.871
>>     1CLC    CHC   31  -0.442  -0.086   0.890
>>     1CLC    C1C   32  -0.317  -0.091   0.824
>>     1CLC    C2C   33  -0.214  -0.193   0.847
>>     1CLC    C3C   34  -0.112  -0.163   0.760
>>     1CLC    C4C   35  -0.154  -0.045   0.688
>>     1CLC    CHD   36  -0.078   0.019   0.591
>>     1CLC    C1D   37  -0.112   0.131   0.520
>>     1CLC    C2D   38  -0.033   0.201   0.421
>>     1CLC    C3D   39  -0.115   0.309   0.380
>>     1CLC    C4D   40  -0.234   0.301   0.455
>>     1CLC    CHA   41  -0.325   0.405   0.430
>>     1CLC    C1A   42  -0.448   0.417   0.491
>>     1CLC    C2A   43  -0.545   0.533   0.476
>>     1CLC    C3A   44  -0.657   0.499   0.577
>>     1CLC    C4A   45  -0.612   0.366   0.634
>>     1CLC    CHB   46  -0.687   0.294   0.727
>>     1CLC   HMB1   47  -0.919   0.099   1.010
>>     1CLC   HMB2   48  -0.868   0.263   0.978
>>     1CLC   HMB3   49  -0.941   0.167   0.851
>>     1CLC    HAB   50  -0.629  -0.151   1.086
>>     1CLC   HBB1   51  -0.831  -0.182   1.180
>>     1CLC   HBB2   52  -0.905  -0.049   1.074
>>     1CLC   HMC1   53  -0.317  -0.294   1.000
>>     1CLC   HMC2   54  -0.143  -0.294   1.018
>>     1CLC   HMC3   55  -0.219  -0.397   0.899
>>     1CLC   HAC1   56   0.029  -0.295   0.831
>>     1CLC   HAC2   57   0.089  -0.162   0.718
>>     1CLC   HBC1   58   0.108  -0.382   0.619
>>     1CLC   HBC2   59  -0.063  -0.406   0.643
>>     1CLC   HBC3   60  -0.006  -0.280   0.536
>>     1CLC   HMD1   61   0.139   0.078   0.430
>>     1CLC   HMD2   62   0.172   0.246   0.397
>>     1CLC   HMD3   63   0.106   0.144   0.272
>>     1CLC    HBD   64  -0.320   0.500   0.234
>>     1CLC   HAA1   65  -0.661   0.476   0.307
>>     1CLC   HAA2   66  -0.512   0.580   0.271
>>     1CLC   HBA1   67  -0.774   0.656   0.383
>>     1CLC   HBA2   68  -0.622   0.762   0.367
>>     1CLC   HMA1   69  -0.751   0.575   0.753
>>     1CLC   HMA2   70  -0.580   0.612   0.740
>>     1CLC   HMA3   71  -0.696   0.698   0.642
>>     1CLC   HED1   72  -0.082   0.795   0.592
>>     1CLC   HED2   73  -0.245   0.827   0.538
>>     1CLC   HED3   74  -0.111   0.846   0.427
>>     1CLC    H11   75  -0.949   0.96

Re: [gmx-users] membedded.gro from g_membed has broken molecules (fix periodicity?)

[Tsjerk Wassenaar]

Hi Peter,

No, you don't need to fix molecules prior to MD.
Fixing them is also not that hard. Build the .tpr, just using the
structure with molecules broken, and then use it as reference
structure to trjconv, with -pbc mol. That will fix the molecules based
on the distances between bonded atoms, which should turn out the way
you want.

Hope it helps,

Tsjerk

On Fri, Apr 8, 2011 at 5:58 AM, Peter C. Lai  wrote:
> The output of g_membed is membedded.gro which appears to have broken lipids
> at the box boundaries, making the box "smooth" (as if g_membed did not fix
> the periodicity of the final frame) when visualized in VMD. How do I fix the
> periodicity for visualization - I cannot use trjconv -s membed.tpr because
> it complains about the missing atoms from the original tpr, as g_membed
> deletes molecules on the fly after calculating the overlaps...
>
> Perhaps more importantly, should I try to make the membedded.gro whole
> before using it as the input coordinate file for the subsequent equilibration
> md? The g_membed paper does not mention this...
>
> Thanks from your neighborhood gromacs noob.
> --
> ===
> Peter C. Lai                 | University of Alabama-Birmingham
> Programmer/Analyst           | BEC 257
> Genetics, Div. of Research   | 1150 10th Avenue South
> p...@uab.edu                  | Birmingham AL 35294-4461
> (205) 690-0808               |
> ===
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] orientational relaxation

[Tsjerk Wassenaar]

Hi Daniel,

If you want to fix the com position, specify the molecule as comm-grps. If
you really don't want movement of the com, and use pressure coupling, first
put the molecule at the origin.

Hope it helps,

Tsjerk

On Apr 12, 2011 7:28 AM, "Mark Abraham"  wrote:

> yes , position restraints of molecules that only allow to orient.
What's your question? Most tutorials will use position restraints at some
stage. There's theory discussion in the manual.

Mark

> > regards. > > --- On Mon, 4/11/11, Mark Abraham 
wrote: >> >> >> From:...

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[gmx-users] Re: EDO and TRS ligand

[Tsjerk Wassenaar]

Ahmet,

Please refrain from sending personal e-mails, unless you're invited to do so.

> I am working on the EDO and TRS ligands for 2/3 weeks.But I dont solved it.
> Please help me.

This is what supervisors are for. I assume you have one.

> I am using the wavefunction spartan 8 program to calculate charges.
> revised_EDO.itp
> ...
> [ moleculetype ]
> ; Name nrexcl
> EDO  3
>
> [ atoms ]
> ;   nr  type  resnr resid  atom  cgnr   charge mass
>  1    OA 1  EDO OAB 1   -0.530  15.9994
>  2 H   1  EDO HAE 1    0.332   1.0080
>  3   CH2 1  EDO CAA 1    0.198  14.0270
>  4   CH2 1  EDO CAC 2    0.198  14.0270
>  5    OA      1  EDO OAD    2    -0.530   15.9994
>  6 H       1  EDO HAF 2     0.332  1.0080
> I didnt change dihedral angel, bond  do I have to change them? I didnt
> arranged for (COH)3(NH3+)C to have charges consistent with its symmetry (TRS
> ligand). I have different charge for CH2 groups, H, O. That is, There is not
> symmetry. What should I do?

There will be symmetry on average, but that does not mean there is
symmetry at every instant, which is what you get from QM calculations.

> can you advice me the other program/software to calculate charge? please do
> not get angry. I do not know what to do. I'm so desperate.

No I can't. You should probably discuss with your supervisor.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] micelles and trjconv -pbc cluster

[Tsjerk Wassenaar]

Hi George,

Recently I wrote an alternative, non-iterative clustering routine, that does
not suffer from convergence failures. If you want, I can send you the
modified trjconv source code. Note that it does not bother about the center
of mass of the cluster, but just builds a network of neighbours, until there
are no more. If you're clusters are not periodic, it won't matter.

Let me know...

Cheers,

Tsjerk

On Thu, Apr 14, 2011 at 4:48 PM, Erik Marklund  wrote:

>  jim jack skrev 2011-04-14 16.42:
>
>   Dear GROMACS users,
>
>I am trying to simulate an SDS micelle in water. As simulation time goes
> by, the micelle approaches the edge of the box and consequently some of
> these molecules get in from the other side. This leads to incorrect radius
> of gyration, eccentricity, etc. A solution to this problem is the option 
> trjconv
> -pbc cluster as described in the page
> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering. In this
> case, the problem is that it takes a lot of time and a huge file (several
> GB) is created due to this procedure. Is there any other alternative?
>
> Thanks in advance
>
> George Koros
>
>I don't think that the cluster option always converges. You could, if
> your micelle is intact at frame 0, first do trjconv -pbc nojump, then
> optionally trjconv -center. That should give a trajectory from which you
> could calculate the radius of gyration. If SDS molecules occationally leave
> the micelle and recombine with a priodic, then you might have a problem with
> the suggested approach.
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,75124 Uppsala, Sweden
> phone:+46 18 471 4537fax: +46 18 511 755er...@xray.bmc.uu.se
> http://folding.bmc.uu.se/
>
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] micelles and trjconv -pbc cluster

[Tsjerk Wassenaar]

Hey :)

As there seems to be interest :)
Below is the diff between native and my version of gmx_trjconv.c 4.5, the
complete source file is attached. I'd fancy comments and suggestions.

Hope it helps,

Tsjerk

###

82a83,208
> static void taw_pbc_cluster(int nrefat,t_topology *top,rvec *x, atom_id
*ndx,
> matrix box,real cutoff)
> {
>   int i,j,id,na,nc,cid,nr,m,*cluster;
>   atom_id *active,*done,*rest;
>   matrix S,T,A;
>   rvec *y,rd;
>   real ax2,ay2,az2,axy,axz,ayz,d,cut2;
>   gmx_bool bClustered;
>
>   cut2 = cutoff*cutoff;
>
>   transpose(box,S);
>   m_inv(S,T);
>   ax2 =   iprod( S[0], S[0] );
>   ay2 =   iprod( S[1], S[1] );
>   az2 =   iprod( S[2], S[2] );
>   axy = 2*iprod( S[0], S[1] );
>   axz = 2*iprod( S[0], S[2] );
>   ayz = 2*iprod( S[1], S[2] );
>
>   snew(rest,   nrefat);
>   snew(active, nrefat);
>   snew(done,   nrefat);
>   snew(cluster,nrefat);
>   snew(y,  nrefat);
>
>   nr = nrefat;
>   nc = m = 0;
>   cid = 0;
>   for (i=0; i   {
> rest[i] = i;
> /* Transform to box coordinates */
> mvmul(T,x[ndx[i]],y[i]);
>   }
>   while (nr)
>   {
> if (nr<0)
>   exit(1);
>
> /*
>If we get here we have _nc_ clustered atoms,
>but none which has neighbours in the rest group:
>Time for a new cluster.
>Pick one atom from the rest group and add it to the clustered ones.
>Rest counter nr is decremented.
>The new active atom is not counted as clustered yet.
>The cluster id was already set.
>When entering the following while loop we have exactly one active
atom.
> */
> done[nc] = rest[--nr];
> cluster[nc] = cid;
> na = 1;
> m  = 0;
> while (na)
> {
>   /*
> Run over active atoms.
> The active atoms run from nc to nc+na
>   */
>
>   /* Iterate over atoms in rest group */
>   for (i=0; i   {
> bClustered = FALSE;
>
> /* For each atom in rest group check distance from active group */
> for (j=nc; j {
>   /* Distance in periodic system in box coordinates */
>   rvec_sub( y[rest[i]], y[done[j]], rd );
>   /* Truncate coordinates for minimial distances */
>   rd[0] -= floor( rd[0] + 0.5 );
>   rd[1] -= floor( rd[1] + 0.5 );
>   rd[2] -= floor( rd[2] + 0.5 );
>   /* Distance follows from d = r'S'Sr = r'Ar = */
>   d =
rd[0]*(rd[0]*ax2+rd[1]*axy+rd[2]*axz)+rd[1]*(rd[1]*ay2+rd[2]*ayz)+rd[2]*rd[2]*az2;
>
>   /* If atom i is within the cutoff distance of j, it is part of the
same cluster */
>   if (d   {
> /* Add the atom to the active cluster group */
> id  = nc+na+m;
> done[id]= rest[i];
> cluster[id] = cid;
> m++;
> /* Relocate the atoms such that it is positioned properly */
> rvec_add(rd,y[done[j]],y[done[id]]);
> /* Now pass on to the next atom in the rest group */
> break;
>   }
>
>   /*
>  We only get here if the atom could not be assigned to a cluster.
>  Then we shift the atom down in the rest array.
>   */
>   rest[i-m] = rest[i];
> }
>   }
>   /* Subtract the number of atoms taken from the rest group */
>   nr -= m;
>   /* Now mark all previously active atoms clustered */
>   nc = nc + na;
>   /* And mark all atoms added active */
>   na = m;
>   m  = 0;
> } /* while (na) */
> cid++;
>   } /* while (nr) */
>   fprintf(stderr,"Found %d clusters",cid);
>
>
>   sfree(rest);
>   sfree(active);
>   sfree(done);
>   sfree(cluster);
>
>   for (i=0; i   {
> mvmul(S,y[i],x[ndx[i]]);
>   }
>
>   sfree(y);
> }
>
638c764
< static real  dropunder=0,dropover=0;
---
> static real  dropunder=0,dropover=0,dclus=0.5;
722c848,851
< "coarse grained ones" } };
---
> "coarse grained ones" },
> { "-dclus", FALSE, etREAL,
> { &dclus },
> "Cutoff distance for clustering" } };
932c1061,1062
< if (0 == top.mols.nr && (bCluster || bPBCcomMol))
---
> /*if (0 == top.mols.nr && (bCluster || bPBCcomMol))*/
> if (0 == top.mols.nr && bPBCcomMol)
1197c1327,1328
<
---
> taw_pbc_cluster(ifit,&top,fr.x,ind_fit,fr.box,dclus);
> /*
1198a1330
> */




On Fri, Apr 15, 2011 at 3:16 AM, Jianguo Li  wrote:

> Hi Tsjerk,
>
> I am doing protein-micelle simultions 

Re: [gmx-users] Adding water to protein to start the simulation process

[Tsjerk Wassenaar]

Hey :)

I see that I never stated to run the production run... But at that point in
the tutorial there have been several equilibration runs already, so it
should be trivial to figure it out. Yet I'll add a small paragraph at the
end of the production run section.
Thanks for the interest in the tutorial. I hope it's good for you.

Cheers,

Tsjerk

On Apr 15, 2011 10:04 PM, "Justin A. Lemkul"  wrote:



Monisha Hajra wrote:

> Hi Justin,
>
> I am trying to follow the protocol only.
>  More than the Gromacs own website, I find
> http://nmr.chem.uu.nl/~tsjerk/course/molmod/md.html#production link is
> more useful.
>
>
Clearly.  This is one of many tutorials linked from the site I posted
before.

 However, I am stuck at one step which is mentioned :
> http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis.html
>
> I am not able to understand how to create traj.trr, traj.xtc and ener.edr
> file. Remaining all is self explained in the previous link.
>
>
These files are output by mdrun, i.e. actually running a simulation.

-Justin

 Really appreciate any help.
>
> Regards
> Monisha
>
> > > > On Fri, Apr 15, 2011 at 8:06 PM, Justin A. Lemkul 
> > > >  jalem...@vt.edu>> ...
>jalemkul[at]vt.edu  | (540) 231-9080
>
> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >
>  ==...
>
>
> >http://lists.gromacs.org/mailman/listinfo/gmx-users >Please
> search the archive at >htt...
>.
>
> >Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >
>
--  Justin A. Lemkul Ph.D. Candidate
ICTAS Doctoral Schol...
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Re: [gmx-users] erorr while using grep command

[Tsjerk Wassenaar]

Hi Sajad,

The error seems quite explicit. The input file to grep does not exist.
Are you in the right directory? Are you mixing op O and 0?

Also, please note that this has nothing to do with gromacs. This is
just your basic linux and this mailing list is the wrong place for
such questions. Furthermore, to omit TPO, you need to run grep -v
'TPO' 10L5.pdb > No-TPO.pdb

Hope it helps,

Tsjerk

On Sun, Apr 17, 2011 at 12:09 PM, Sajad Ahrari  wrote:
> hello every one!
> I am trying to omit TPO(witch stands for phospho-tyrosine) from my pdb file
> by executing the command"grep TPO 10L5.pdb > TPO.pdb". but i am being facing
> with this erorr"grep: 10L5.pdb: No such file or directory" can any one help?
>
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] ask for help on connection to vpn from two computers

[Tsjerk Wassenaar]

Hi Delara,

This isn't really the place for these kind of questions, is it? Why not ask
the system admins of your network?

Cheers,

Tsjerk

On Apr 18, 2011 9:11 AM, "delara aghaie"  wrote:


Dear gromacs users
I connect via vpn to the university which I run my jobs using gromacs on its
HPC system. I have Id & password for that.
now I want to know if I can connect from two computers in my lab to the vpn
connection at the same time with one ID and password?

the computers are not connected to each other.

Thanks
D.Aghaie




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Re: [gmx-users] fetal erorr while running" pdb2gmx" command

[Tsjerk Wassenaar]

Hey Sajad,

That sounds quite serious, having a fetal error
(http://www.thefreedictionary.com/fetal)!

But it seems you just have a missing atom, as is indicated in the
output. Check the structure before trying to convert it. In
particular, read the sections in the PDB file starting with 'REMARK
465' and 'REMARK 470'.

Surely you'd also been able to find this in the FAQ or in the
archives. Please search there before posting.

Hope it helps,

Tsjerk

On Mon, Apr 18, 2011 at 10:27 AM, Sajad Ahrari  wrote:
> dear users
> after running the command "pdb2gmx -f 1OL5.pdb -o 1OL5.gro -water spc" ,i
> was faced with the erorr: "Fatal error: Atom CG not found in residue seq.nr.
> 251 while adding atom". i used Gromacs 4.5.3
> with AMBER99SB force field. it seems that some atomes are missing.should i
> be modeling the protein to have all it's atoms? is Gromacs have any features
> to correct the missing ones?
> thanks!
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] saving coordinates

[Tsjerk Wassenaar]

Hey :)

With domain decomposition the particles are saved with the coordinates
corresponding to the position in the rectangular brick with sides equal to
the diagonal elements of your unit cell. With particle decomposition the
positions are taken for which holds that the first atom of the molecule the
particle is part of is in that box.

Cheers,

Tsjerk

On Apr 19, 2011 4:43 PM, "Justin A. Lemkul"  wrote:

Nilesh Dhumal wrote: > > Hello Justin, > > THanks for your reply. > >
Suppose any atom that leaves...
Presumably.  Look in the code, but I suspect this is indeed the case and the
reason why trjconv -pbc nojump and other such operations are useful.

-Justin

> Nilesh > > On Wed, April 13, 2011 9:26 pm, Justin A. Lemkul wrote: > >>
Nilesh Dhumal wrote: >> ...
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Re: [gmx-users] Coarse-grained force field

[Tsjerk Wassenaar]

Hi Ksenie,

I don't think you'll be able to find a proper atomistic force field
description for lanthanide either. Check
http://www.gromacs.org/Documentation/How-tos/Parameterization.

But in general, no, you can't mix force fields, and definitely not
ones of different resolution. In addition, think of what it means, a
coarse grained ion. Usually it's either something that binds one part
of a protein to another (emulate with some bonds), or it is a sphere
of water with something in it that happens to bear some charge, like
in the ion definitions in Martini.

Cheers,

Tsjerk

On Wed, Apr 20, 2011 at 7:54 AM, ksenia248  wrote:
> Hello. I am trying to simulate the supramolecular organization of liquid
> crystalline complex of lanthanide by coarse-grained molecular dynamics. But
> I have some problems with force fields. I can not find coarse-grained force
> field for lanthanide ion. Can I use atomistic force field oplsaa.ff for
> lanthanide ion and Martinin force field for other groups of atoms together
> in one simulation? Or may be you can recommend me some other coarse-grained
> force fields? Thank you very much.
> --
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: 答复: [gmx-users] any software which could convert a polypeptidesequence to a pdb file?

[Tsjerk Wassenaar]

Hi,

Pymol is sort of semi commercial. You can install it easily on Ubuntu,
using apt-get install pymol (free!), you can install from source (also
free!). You can obtain an educational build (also free!, though
requiring registration). Any will do for the building of sequences,
which on linux is as simple as running:

for i in Y W F A; do for j in Y W F A; do for k in Y W F A; do for l
in Y W F A; do
PEP=H$i$j$k$lPAS
pymol -qcd "editor.build_peptide('${PEP}');cmd.save('$PEP.pdb')"
done; done; done; done

Hope it helps,

Tsjerk


2011/4/20 Terry :
>
> Hi Chuan,
> Leap is a part of Ambertools which is free.
> See http://ambermd.org/#AmberTools
> Good luck.
> Terry
>
> 2011/4/20 Liao Chuan 
>>
>> HI, Itamer and Mark, thanks for your prompt replies.
>>
>> Pymol, Amber and Sybyl are commercial software. Any free software/scripts?
>>
>>
>>
>> - Chuan
>>
>>
>>
>> 
>>
>> 发件人: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
>> 代表 Mark Abraham
>> 发送时间: 2011年4月20日 13:31
>> 收件人: Discussion list for GROMACS users
>> 主题: Re: [gmx-users] any software which could convert a polypeptidesequence
>> to a pdb file?
>>
>>
>>
>> On 4/20/2011 2:36 PM, Liao Chuan wrote:
>>
>> Dear gmx-users,
>>
>> I want to conduct simulations of a protein and its ligand, a heptapeptide
>> HXXXPAS, where X could be tyrosine, tryptophan, pheny alanine, alanine.
>> Thus, I will have to conduct a total number of 4*4*4=64 runs. I've got the
>> pdb file of the protein, but I have no idea how to prepare the pdb files of
>> those 64 heptapeptides with sequences already known. Is there any
>> software/script which could convert a polypeptide sequence to a pdb file?
>>  Any comment is appreciated!
>>
>> Leap in the AmberTools package is good for this.
>>
>> Mark
>>
>> --
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>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] trjcat eneconv time continuation

[Tsjerk Wassenaar]

Hi David,

You should have as many lines with a 'c' as you have trajectories.

Cheers,

Tsjerk

On Apr 25, 2011 3:51 PM, "David Rodríguez" 
wrote:



2011/4/25 Mark Abraham  > > On 4/25/2011 8:42 PM,
David Rodríguez wrote: >>...

Sorry that my query wasn't detailed enough. Trjcat yields a Fatal error
(Error reading user input). Here is what I tried, considering the first 2
trajectories (the errors are the same if you consider more than that):

Option 1:
echo c | trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime

Option 2:
trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime << EOF
c
EOF

Option 3:
trjcat -f traj1.xtc traj2.xtc -o traj_1_2.xtc -settime < choice.txt

Where 'choice.txt' contains the letter 'c' in one line.
The log in any case is the following:



  :-)  /opt/gromacs405/bin/trjcat  (-:

Option Filename  Type Description

  -f  traj1.xtc  Input, Mult.
  traj2.xtc   Trajectory: xtc trr trj gro g96 pdb cpt
  -o   traj_1_2.xtc  Output, Mult. Trajectory: xtc trr trj gro g96 pdb
  -n  index.ndx  Input, Opt.  Index file
-demux remd.xvg  Input, Opt.  xvgr/xmgr file

Option   Type   Value   Description
--
-[no]h   bool   no  Print help info and quit
-niceint19  Set the nicelevel
-tu  enum   ps  Time unit: ps, fs, ns, us, ms or s
-[no]xvgrbool   yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-b   time   -1  First time to use (ps)
-e   time   -1  Last time to use (ps)
-dt  time   0   Only write frame when t MOD dt = first time (ps)
-precint3   Precision for .xtc and .gro writing in number of
decimal places
-[no]vel bool   yes Read and write velocities if possible
-[no]settime bool   yes Change starting time interactively
-[no]sortbool   yes Sort trajectory files (not frames)
-[no]keeplast  bool no  keep overlapping frames at end of trajectory
-[no]cat bool   no  do not discard double time frames

Reading frame   1 time   50.000


Enter the new start time (ps) for each file.
There are two special options, both disable sorting:

c (continue) - The start time is taken from the end
of the previous file. Use it when your continuation run
restarts with t=0.

l (last) - The time in this file will be changed the
same amount as in the previous. Use it when the time in the
new run continues from the end of the previous one,
since this takes possible overlap into account.

  File Current start (ps)  New start (ps)
-
traj1.xtc0.000 ps
traj2.xtc0.000 ps
---
Program trjcat, VERSION 4.0.5
Source code file: gmx_trjcat.c, line: 178

Fatal error:
Error reading user input
---

"Yeah, a Wuzz, Or a Jerk" (F. Black)



This is with version 4.0.5, when using version 4.5 the log only differs in
the line of the code where the error occurs (201 instead of 178).

Best,
David.

> > Mark > > > > -- > gmx-users mailing listgmx-users@gromacs.org >
http://lists.gromacs.org/ma...





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Re: [gmx-users] trjcat eneconv time continuation

[Tsjerk Wassenaar]

Hi David,

Sorry for reading half... 'echo c c | trjcat ... ' should work.

Cheers,

Tsjerk

On Apr 25, 2011 6:02 PM, "David Rodríguez" 
wrote:


2011/4/25 Tsjerk Wassenaar  > > Hi David, > > You should
have as many lines with ...
Sure Tsjerk!

Now options 2 and 3 (not 1) work, just that easy. Thank you so much.

Best,
David.

>> >> On Apr 25, 2011 3:51 PM, "David Rodríguez" 
wrote: >> >> >> >> 201...




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Re: [gmx-users] g_rmsf

[Tsjerk Wassenaar]

Hi Efrat,

2011/5/3 Efrat Noy :
> Hi,
>
> I have 2 questions regarding root mean square fluctuation calculations:
>
> 1. what exactly is the difference between the values in the rmsf.xvg file
> and the values in the rmsdev.xvg file (obtained with the -od option)? Are
> the rmsf.xvg values are standard deviations of atom positions along the
> trajectory with respect to an average structure of the trajectory? And
> rmsdev.xvg values are the same but in respect to a reference structure
> defined by the tpr file?

The help is pretty clear on the first part: -od gives the RMSD w.r.t.
the reference. You're right on the nature of the RMSF.

>
> 2. Is it possible to fit the trajectory structures, prior to rmsf
> calculations, on only part of the protein?

Yes. You can preprocess the trajectory with trjconv and use the -nofit
option to g_rmsf.

Cheers,

Tsjerk

> Thanks, Efrat
>
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Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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The Netherlands
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Re: [gmx-users] trjconv center on protein

[Tsjerk Wassenaar]

Hey :)

Option -center shifts the system, which will show up as a component in the
displacement.

Cheers,

Tsjerk

On May 6, 2011 5:39 PM, "Justin A. Lemkul"  wrote:

Tomek Wlodarski wrote: > > Dear Justin, > > Thanks, sure I will give more
details. > > This comman...
Are all the measurements being done in VMD, or are you using g_dist for any
of these?  If you're using g_dist, then some of the distances may be
affected by using your old .tpr file, wherein the protein is perhaps not
centered.

If all of the measurements are being done in VMD, then I can't comment, but
perhaps someone else can.  It might be useful to show how you're doing these
measurements.  If you're not using g_dist, it would be interesting to see
how the results of g_dist and VMD compare, in order to tease out the source
of the difference.

-Justin

> Best! > > tomek > > On Fri, May 6, 2011 at 1:15 AM, Justin A. Lemkul <
jalem...@vt.edu> wrote: >>...
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Re: [gmx-users] g_sas query

[Tsjerk Wassenaar]

Hey Anirban,

I would consider the ions part of the solvent. But the procedure is right.

Cheers,

Tsjerk

On May 7, 2011 7:35 AM, "Anirban Ghosh" 
wrote:

Hi ALL,

I want to calculate the SASA of a protein embedded in a bilayer along with
water and ions. So while using g_sas I understand that I need to supply all
non-solvent atoms as calculation group and Protein as the output group. So I
need to make a group with Protein+Lipid+Ions as the calculation group.
Right?
Thanks a lot in advance.

Regards,

Anirban

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Re: [gmx-users] How to recenter solvent around solute

[Tsjerk Wassenaar]

Hi,

Justin is very right to point at the workflow. In your case, the
points 5 and 6 apply: centering, and putting things in some box. Maybe
that doesn't work in one pass and you'll have to use trjconv twice.

>> This does not work. Neither is the solute always surrounded by solvent for
>> every frame (it goes out of the box) nor is the original unit cell
>> (truncated octahedron) preserved.

You have to think out of the box with PBC :) The solute is always
surrounded by solvent, except where it touches its own image, in which
case you should consider throwing away and redo the run in a larger
box. There is no out of the box where atoms can go to. Furthermore,
the unit cell does not have shape, it only has translational relations
(lattice vectors). You can carve out any general shape you want, such
as rectangular, truncated octahedron, rhombic dodecahedron. Note that
only in special cases you can carve out regular instances of those
(such as a cube for a rectangular brick).
To understand this, here's a bit of an exercise:

Draw three identical hexagons in contact with each other
>From one of the hexagons, draw vectors to the other two, and draw the
parallellogram spanned by these vectors.
Place a hexagon at the farthest node, and not how the parallellogram
has exactly the same content as any of the hexagons.
Now turn the parallellogram into a rectangular brick by translating a
part of it, and note how the brick still has the same contents as a
hexagon.
Feeling confident that any shape will do, find some tilings from
Escher and try to see how you can fit that into a parallellogram,
rectangle, or hexagon :) Of course the coolest would be to use those
to define a unit cell to put your atoms in :p

Groetjes,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] problem in multichain protein solvation

[Tsjerk Wassenaar]

Hi,

> I tried to solvate an assembly of amyliod peptides (16 peptide), using
> editconf and genbox respectively as follow,
> editconf -f rotated.gro  -box  76 6 6 -center 0 0 0  -o rotated-box
>
> Nothing here does any rotation.

Well, it seems something that was rotated goes in... that seems fine.

> Sounds like the combination of your input coordinates, specification of the
> center and box sizes places the protein outside the box.

The specification of -center 0 0 0 will result in the center of
geometry of your chains to be placed at the origin. Your box will
start at the origin, so doing this by definition will place the
majority of your system outside of the box. Then again, if you process
it like you would for simulation, you will find it doesn't matter, as
there is no outside out of the box.

> So, what do you suggest?

Read more, in particular regarding periodic boundary conditions and go
on with the next step in your protocol.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] pressure in NPT and NVT

[Tsjerk Wassenaar]

Hi Nilesh,

You don't state the size of your system and the length of your simulations,
which are highly relevant in relation to your observations. In any case, you
should consider that your simulation is but a single sample, drawn from a
distribution of possible paths, and it is probably quite reasonable to find
it off by a few bar if the simulation is short and/or the system size is
small.

Hope it helps,

Tsjerk

On May 13, 2011 3:07 PM, "Justin A. Lemkul"  wrote:

Nilesh Dhumal wrote: > > Hello, > > I am using NPT simulation for water -
spce model (opls-aa forc...
Probably the system is not yet equilibrated.

> > For NVT simulatin I get the value around average pressure 710.685 bar. >
> I am running the si...
Because the box is fixed.  It cannot respond to internal forces in your
system.  Pressure values during NVT don't mean much.

-Justin

> I am using gromacs version 4.0.7. > > Thanks > > Nilesh > --


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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Re: [gmx-users] R: gmx-users Digest, Vol 85, Issue 101

[Tsjerk Wassenaar]

Hi  Anna,

You can also renumber the xvg file:

awk 'BEGIN{N=1}/^[^@#]/{print N++, $2}' file.xvg > renum.xvg

Hope it helps,

Tsjerk

On May 13, 2011 3:51 PM, "Anna Marabotti"  wrote:

Dear Mark,
thank you also for your suggestion, indeed using the nvt.gro file with the
sequential numbering I was able to distinguish the contributions from both
chains, instead of seeing them superimposed.
Now I have another question. I used pdb2gmx to prepare another file for
simulation (it is the same protein as above, with a mutation). The pdb file
contains two identical chains numbered starting from 21 to 379, marked with
chain ID A and B.
Using the command line:
pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top
I obtained a .gro file in which the numbering correctly starts from 21 to
379 in both chains, but no chain ID is present. I also tried to use
-chainsep, but nothing changed. So my (last) question is: is there any way
to avoid renumbering the file, but without obtaining a superposition of
residue numbers in both subunits? In other workds: is there a possibility to
leave some form of "chain identifier" in the .gro file? Or the only way to
obtain unambiguous identification of each residue is to renumber the file?
Thank you very much
Anna


Date: Fri, 13 May 2011 22:34:17 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] numbering of .gro file
To: Discussion list for GROMACS users 
Message-ID: <7690ae4b5380.4dcdb...@anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"



On 13/05/11, Anna Marabotti   wrote:
>
> Dear
> gmx-users,
>
> I'm simulating a
> homodimeric protein obtained by homology modelling. In the .pdb file, I
have 2
> chain identifiers (A and B). I used Gromacs 4.0.7 to prepare the .gro
files for
> simulation (up to nvt); then I was forced to switch to Gromacs 4.5.4 on
another
> machine to continue with npt and full MD. I used the files from Gromacs
4.0.7 to
> continue, and it seems to me that all went OK. Now I have the files from
the
> full MD, and I started to analyze them.
>
> I used g_rmsf to
> analyze the fluctuations of the residues, and I found that the results for
the
> two subunits of the protein are superimposed. In the file .gro that comes
from
> the MD as well as in the file .gro that comes from the npt MD made with
Gromacs
> 4.5.4, the number of residues of the second subunit does not continue
after the
> first subunit (i.e. after the last 359th residue of the first subunit, I
see
> that the first residue of the second subunit is numbered 1 instead of
360), but
> in the nvt file produced by Gromacs 4.0.7 that I provided to Gromacs
> 4.5.4, the numbering of the two subunits is
> sequential.
>
> My questions
> are:
>
> 1) why Gromacs 4.5.4
> changed the numbering of the residues in the two subunits, even if it
started
> from a .gro file?
>
>
>
>

The trajectory files do not number the atoms, so the only way you can
generate such numbering is by matching them with a structure file that also
has such numbering. It's hard to be any more specific in the absence of
command lines. If you just match the trajectory file with a more suitably
numbered structure file (with atom ordering preserved) then everything is
fine.


>
>
>
>
>
> 2) Does this affect
> the result of the MD?
>
>
>
>

I highly doubt it.


>
>
>
>
>
> 3) how can I
> separate, or renumber, the resulting .gro files in order to have a graph
in
> which the fluctuations are not superimposed?
>
>
>
>

I rather expect that the input file to your NPT grompp had this "feature".
In any case, you need to identify where it first arose in your workflow in
order to work out why it happened and what to do about it.

Mark

>
>
>
>
>
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[gmx-users] Fwd: Question => g_anaeig -first -last

[Tsjerk Wassenaar]

Hi Lin,

As these questions are not directly related to the tutorial, the
gromacs user list is the better place for them.

There are indeed as many eigenvectors in the .trr file as there are
-values in the .xvg file, and they are matching series.

The files you get for the extreme projections correspond to the set of
eigenvectors specified through -first to -last. In your case that
means the first ten eigenvectors.

The covariance matrix is positive semidefinite, which means that it
may have eigenvalues equal to zero. In your case, you'll get six zero
eigenvalues for the six degrees of freedom you remove by fitting the
trajectory. Due to limited numerical precision, these may turn out
slightly negative.

Cheers,

Tsjerk


-- Forwarded message --
From: Chih-Ying Lin 
Date: Mon, May 16, 2011 at 4:33 AM
Subject: Question => g_anaeig -first -last
To: Tsjerk Wassenaar 




Hi Tsjerk:
I am doing your Tutorial and have a question about g_covar and a_anaeig.
I issued the following two commands.
g_covar_mpi -s 1LW9-MD.tpr -f 1LW9-MD.xtc -o eigenvalues.xvg -v
eigenvectors.trr -ascii covariances.dat
g_anaeig_mpi -v eigenvectors.trr -s 1LW9-MD.tpr -f 1LW9-MD.xtc -first
1 -last 10 -extr extreme-first-last.gro

There are 1476 eigenvalues in the eigenvalues.xvg and they are listed
from the max to min.
I supposed there are 1476 eigenvectors in eigenvectors.trr , right 
Are those eigenvectors are listed corresponding to the the list of the
eigenvalues from the max to min 
For the command, g_anaeig -first 1  -last 10  .. , I will get 10
sets of .gro files.
Will those structures in the .gro files correspond to the top 10
eigenvalues 

By the way, there are 6 negative eigenvalues in the eigenvalues.xvg.
I don't know why because you told me all eigenvalues are positive 
Thank you very much
Lin










-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] "Command Not Found"

[Tsjerk Wassenaar]

Hi Natalie,

You're in the wrong place, and probably trying the wrong thing. The
FDAtools are not part of Gromacs and if you encounter issues with them
you should raise it with the authors. They may have a user list too.

Aside from that, the FDAtools seem to be an R package. That means that
they will offer you extended functionality within R, and not as
command line tools.

Cheers,

Tsjerk



On Mon, May 16, 2011 at 5:01 PM, Natalie Stephenson
 wrote:
> Sorry for the confusion - didn't mean I'd used a wildcard when typing the 
> commands ... just meant I get that response for both commands.
>
> They're an add on created from a the Molecular BioMechanics group 
> (http://projects.eml.org/mbm/website/fda_gromacs.htm) - I've downloaded 
> they're software as they mention:
>
> Installing the FDAtools package:
> FDAtools depends on bio3d and SparsM. Please download the bio3d package.
> A a Mac / Linux user, check that your R_LIBS variable points to the folder in 
> which packages should be installed (insert an export R_LIBS="..." in your 
> .profile / .bashrc if not previously done).
> Install bio3d by executing 'R CMD INSTALL bio3d_1.0-6.tar.gz'.
> Install SparseM by executing 'install.packages("SparseM")' in an R console.
> Now we are ready to install FDAtools, just type 'R CMD INSTALL 
> FDAtools_0.9.tar.gz' on the command line.
>
> And downloaded the 'gromacs_4.0.5_pf' that they have (FDA-Gromacs).  Is it 
> likely to be some problem with the FDA-Gromacs package installation (the one 
> I mentioned below) ... or is it likely to be something else?
>
> Thanks
> Natalie
>
> 
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
> of Justin A. Lemkul [jalem...@vt.edu]
> Sent: 16 May 2011 15:56
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] "Command Not Found"
>
> Natalie Stephenson wrote:
>>  Hi All,
>>
>> Sorry to bug you all about this - it's been mentioned a few times but I
>> can't find an answer that seems to relate to the situation I've got.
>>
>> I'm trying to use the g_fdaconv / g_fdatools within gromacs 4.0.5,
>> however, everytime I type the commands I get 'g_fda*: command not found'.
>>
>
> Using wildcards will not find command names.
>
>> These are present in the /usr/local/gromacs/bin directory - however when
>> I've checked over the config.log they haven't installed.  I'm not sure I
>
> OK, so you have an executable installed, but it didn't install?  Can you 
> please
> clarify?  Neither g_fdaconv or g_fdatools are standard Gromacs utilities - are
> they some sort of external package or add-on?
>
> -Justin
>
>> understand what's happened - the installation was done by downloading
>> followed by ./configure, make, make install, and everything else seems
>> to be functioning fine.  What is it I've missed?
>>
>> Can anyone shed any light on my (probably completely stupid) problem?!
>>
>> Thanks loads,
>> Natalie
>>
>> 
>> Natalie Stephenson, B.Sc
>> PhD Research Associate
>>
>> Manchester Interdisciplinary Biocentre
>> 131 Princess Street
>> Manchester
>> M1 7DN
>> x65816
>> 
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] mirroring a trajectorie

[Tsjerk Wassenaar]

#!/usr/bin/env python

# Python compliant e-mail
# Save it as xtcrev.py

# Hi Thomas,

# Here's a piece of python code that reverses a trajectory.

### xtcrev.py: ###

#!/usr/bin/env python

# Reverse an XTC trajectory
#
# (c)2011 Tsjerk A. Wassenaar
#   University of Groningen
#

from struct import unpack
import sys
import os

def i(x): return sum([ord(x[j])<<(24-j*8) for j in range(4)])

def strseek(stream,s,bufsize=1):
v = len(s)
x = stream.read(bufsize)
n = 0
while len(x) >= v:
m = x.find(s)
if m > -1:
# If we found the tag, the position is the total length
# read plus the index at which the tag was found
n += m
yield n
# Now we strip the part up to and including the tag
x = x[m+v:]
n += v
elif len(x) > v:
# If the tag was not found, strip the string, keeping only
# the last v-1 characters, as these could combine with the
# next part to be read in.
# n is incremented with the number of characters taken from
# the current string x (len(x)-v+1)
n += len(x)-v+1
x = x[1-v:]
if len(x) <= v:
x += stream.read(bufsize)

# Get the tag to identify the start of a frame
f   = open(sys.argv[1])
tag = f.read(8) # Tag: magic number and number of atoms
n   = 92 + i(f.read(84)[-4:])   # Size of frame in bytes
f.close()

# Find all positions at which the tag is found and the frame lengths
frames  = [ i for i in strseek(open(sys.argv[1]),tag) ]
nf  = len(frames)
lengths = [ j-i for i,j in zip(frames,frames[1:]+[nf]) ]

# Reverse the lists
frames.reverse()
lengths.reverse()

# Write the frames in reversed order
f = open(sys.argv[1])
o = open(sys.argv[2],"w")
for pos,bytes in zip(frames,lengths):
f.seek(pos)
o.write(f.read(bytes))
f.close()
o.close()

sys.exit()





On Tue, May 17, 2011 at 6:05 PM, Thomas Schlesier  wrote:
> Hi all,
> is it possible to mirror a trajectorie?
>
> I have done pulling simulations, where i first pulled two molecules apart
> and later used the pulled them together (starting form the last frame of the
> pulling-(apart)-simulation).
>
> Now want to calculate the rmsd of structures for the path. So i would like
> to compared first frame of pull-apart with last frame of pull-together ...
>
> Only way i could think of, would be to write the .xtc into individual
> .gro-files, then order them and finally put them together to the mirrored
> .xtc
> This should work, but probably there is an easier way of doing this?
>
> Greetings
> Thomas
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Re: [gmx-users] average trajectory

[Tsjerk Wassenaar]

Hey,

If you can sum them, the only thing needed afterwards is updating the
color labels. Like per awk (dividing by two):

 awk -F\" '/#/{$4=$4/2}1' file.xpm

Cheers,

Tsjerk

On Thu, May 19, 2011 at 2:43 PM, Erik Marklund  wrote:
> Justin A. Lemkul skrev 2011-05-19 14.30:
>>
>>
>> Yulian Gavrilov wrote:
>>>
>>>
>>> Dear gromacs users,
>>> 1. I have got 3 MD-outputs for the same protein (3 runnings for 100 ns).
>>> I want to make a distance matrix (*g_mdmat*) for the average trajectory
>>> of these 3 runnings.  *g_mdmat* gives an average  matrix for one trajectory,
>>> but I want to get it for the average trajectory.
>>> I tried to use *xpm2ps* to get average matrix, but in it I can only
>>> combine matrices (not to take an average matrix).
>>> Can I get an average matrix, or an average trajectory?
>>>
>>>
>>
>> I have thought about doing this myself, but have never attempted it.
>>  There is no Gromacs tool that will do such operations on .xpm files.  The
>> best I could figure would be to write an external script that:
>>
>> 1. Translates the .xpm matrix to numerical values based on the the header
>> information
>> 2. Takes the average at each position in the matrix
>> 3. Writes a new .xpm file
>>
>> -Justin
>
> I remember using imagemagick tools (composite?) to make average matrices
> from xpm files. I don't remember exacly how I did it though, and it may have
> required hacking the palette in the xpm files before combining them.
>
> Cheers,
>
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> er...@xray.bmc.uu.se    http://folding.bmc.uu.se/
>
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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Re: [gmx-users] Domain Motion => How do get the rotational axis from eigenvectors ?

[Tsjerk Wassenaar]

Hi Lin,

You don't get such axes directly from covariance analysis. If you want
to know which rotations are associated with a certain eigenvector, you
have to run a routine like dyndom (http://fizz.cmp.uea.ac.uk/dyndom/)
on the extreme projections of your trajectory onto an eigenvector.

Cheers,

Tsjerk

On Fri, May 27, 2011 at 4:54 AM, Chih-Ying Lin  wrote:
>
> Hi
> I want to protein's domain motion.
> I use   g_covar    and    g_anaeig  to get the eigenvectors.
> How can i get the rotational axis of which protein do its domain motion from
> those eigenvectors?
> I found the papers and the authors plot its rotational axis of domain
> motion.
> How did they make it ?
>
> Thank you
> Lin
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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Re: [gmx-users] Minimum periodic distance

[Tsjerk Wassenaar]

Hi Kavya,

> "shortest periodic distance is 1.39714 (nm) at time 21824 (ps),
> between atoms 2062 and 3688"
> where 2062 is a protein atom and 21824 is a water molecule.

21824 is the time in ps at which the two atoms indicated, 2062 and
3688, are at the short distance given. You can dump the frame with
trjconv and have a look. Probably your molecule stretched, or you
solvated in a rectangular box and the protein rotated. In the first
case, set a larger distance, in the second, use a rhombic
dodecahedron.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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Re: [gmx-users] is it possible to convert NAMD psf file to gromacas format?

[Tsjerk Wassenaar]

Hey,

>> If a rename atom A into B, it will mix the old atom B which already there
>> before A renamed into B. However, if the old atom B also need to be renamed
>> into C. Here is the problem , command cannot recognize this atom B is the
>> new generated or the old atom B. Of course, those atom B derive from A
>> should not be renamed into C.
>
> Do two passes of sed per the earlier suggestion. Do B->C, then A->B.

sed -e 's/B/C/' -e 's/A/B/' file.in > file.out

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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Re: [gmx-users] GTG to GAG with amber FF99SB force field

[Tsjerk Wassenaar]

Hi Lishan,

Your mail would be a bit more readable with more structure...

Anyway, it says in the manual you can't do perturbation on the
multiplicity. That makes sense, because interpolation from 1 to 3 goes
through a whole series of rational numbers, but you can't have
non-integer periods... If you must, you first have to remove the
dihedral, i.e. bring the amplitude to 0, and then raise again to the
other function.

Cheers,

Tsjerk

On Mon, May 30, 2011 at 3:15 AM,   wrote:
> Dear Gromacs users: I use gromacs.4-5-3 to calculate the free energy changes
> for the GTG to GAG alchemy process, where charge annihilation is performed
> first followed by soft core VDW calculation. When doing the soft core VDW
> calculation, I see this error message ?Fatal error: [ file gtg_vdw.top, line
> 314 ]: Proper Dih. multiplicity can not be perturbed 1.00!=3.00?.
> Line 314 has the following content ?17 16 18 24 9? The atoms with VDW radius
> and well depth changes include 20 CT 3 THR CG2 20 -0. 12.01 CTD 0.0
> 12.01 ; qtot 0.0439 21 HC 3 THR HG21 21 0. 1.008 HCD 0.0 1.008; qtot
> 0.1081 22 HC 3 THR HG22 22 0. 1.008 HCD 0.0 1.008; qtot 0.1723 23 HC 3
> THR HG23 23 0. 1.008 HCD 0.0 1.008; qtot 0.2365 24 OH 3 THR OG1 24
> -0. 16 OHD 0.0 16 ; qtot -0.4396 25 HO 3 THR HG1 25 0. 1.008 HOD 0.0
> 1.008; qtot -0.0294 Atom types CTD, HCD, OHD, HOD are defined in a separate
> file and included in the topology file. My question is how to solve this
> problem and a related question is whether the overall setup is correct.
> Best, Lishan
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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The Netherlands
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Re: [gmx-users] Minimum periodic distance

[Tsjerk Wassenaar]

Hi Kavya,

There is no way to correct for such things afterwards. But I would
guess it's not much of a problem in your case. If a situation with a
short distance is only transient, it is unlikely to affect the
simulation. On the other hand, you may have secondary, indirect
effects due to water ordering. Whether that is problematic in your
case is something you'll have to assess yourself.

Cheers,

Tsjerk

On Mon, May 30, 2011 at 12:24 PM, Kavyashree M  wrote:
> Hello Sir,
>
> The difference between the rcolumb (1.4nm) and minimum image distance
> that was obtained between two hydrogen HZ2 and HZ3 atoms of 2 lysine
> residues (1.39714nm) is 0.00286nm = 0.0286Ang,
> Since this distance is smaller than bond distance between hydrogen and
> nitrogen which is ~1.0Ang, So will this effect the results of the
> simulations?
> Kindly let me know whether I need to redo the simulation again? or is there
> any way to correct this or can it be ignored?
>
> Thanking you
> With regards
> M. Kavyashree
>
>
> On Mon, May 30, 2011 at 10:36 AM, Kavyashree M  wrote:
>>
>> Hello sir,
>>
>> I had used a dodecahedron cell for simulation. I have run
>> the simulation for 100ns, did you man I have to restart the
>> simulation again?
>>
>> Thanking you
>> Kavya
>>
>> On Sun, May 29, 2011 at 5:40 PM, Tsjerk Wassenaar 
>> wrote:
>>>
>>> Hi Kavya,
>>>
>>> > "shortest periodic distance is 1.39714 (nm) at time 21824 (ps),
>>> > between atoms 2062 and 3688"
>>> > where 2062 is a protein atom and 21824 is a water molecule.
>>>
>>> 21824 is the time in ps at which the two atoms indicated, 2062 and
>>> 3688, are at the short distance given. You can dump the frame with
>>> trjconv and have a look. Probably your molecule stretched, or you
>>> solvated in a rectangular box and the protein rotated. In the first
>>> case, set a larger distance, in the second, use a rhombic
>>> dodecahedron.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>>
>>> --
>>> Tsjerk A. Wassenaar, Ph.D.
>>>
>>> post-doctoral researcher
>>> Molecular Dynamics Group
>>> * Groningen Institute for Biomolecular Research and Biotechnology
>>> * Zernike Institute for Advanced Materials
>>> University of Groningen
>>> The Netherlands
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>>
>
>
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] flexibility

[Tsjerk Wassenaar]

Hi,

The usual (statistical) way to compare fluctuations (variances) is by
taking the ratio (i.e. of the MSFs, not the RMSFs). Maragliano e.a.
(BiophysJ 2004) wrote on such comparison of fluctuations, using a
variance ratio test.
In your case, you'd have to combine it with a structure alignment to
find which numbers should be compared with which.

Cheers,

Tsjerk

On Wed, Jun 1, 2011 at 1:24 PM, Justin A. Lemkul  wrote:
>
>
> shiva birgani wrote:
>>
>>    Message: 1
>>    Date: Tue, 31 May 2011 06:56:16 -0400
>>    From: "Justin A. Lemkul" mailto:jalem...@vt.edu>>
>>    Subject: Re: [gmx-users] flexiblity
>>    To: Discussion list for GROMACS users >    >
>>    Message-ID: <4de4c950.70...@vt.edu >
>>    Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>>
>>
>>    shiva birgani wrote:
>>     > Dear all
>>     > I have simulated two different proteins (A and B). I need to compare
>>     > their flexibility. RMSF help to examine their flexibilty
>>    individually,
>>     > but I want to campare them with each other.
>>     > Do anybody know a solution to this? Would you please help me in
>>    this regard?
>>     >
>>
>>    Is it not just a matter of comparing the RMSF between the two proteins?
>>
>>    -Justin
>>
>>    --
>>    
>>
>> Dear Justin
>>
>> Yes I want to compare them, but I am not sure that RMSF is appropriate
>> test to comparison, because two proteins are completely different in their
>> amino acid contents and numbers.
>>
>
> RMSF is the correct metric for measuring the flexibility of your proteins.
>  How you then interpret the data in light of what's known about your system
> and the goals of your study is up to you.  All part of good experimental
> design.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] g_covar

[Tsjerk Wassenaar]

Hi Kavya,

Each atom has three coordinates; 3*3740=11220 coordinates, yielding as
many eigenvalues and -vectors.

Cheers,

Tsjerk

On Wed, Jun 1, 2011 at 2:44 PM, Kavyashree M  wrote:
> Dear users,
>
>  I was using g_covar (gmx 4.5.3) to find the eigenvalue and
> eigenvectors. When I used for "protein" which is actually - 3740 in
> number, it gave a total of 11220 eigenvalues, similarly for bacbone,
> c-alpha atoms, the number of eigenvalues given was not matching
> with the number of atoms in question.
> I presume that the number of eigenvalues generated should correspond
> to the number of atoms considered in question.
> But the xpm file generated corresponds with the query given ie., protein,
> C-alpha or backbone as expected.
>
> Kindly clarify my doubts.
>
> Thank you
> With regards
> M. Kavyashree
>
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Solvating dodecahedron

[Tsjerk Wassenaar]

Hi Justin,

> Note that the pseudo-sphere representation is for visualization
> purposes only; the triclinic cell should be the input for any simulation.

This not true. It doesn't matter which representation you use as
input. Molecules may be broken over PBC, but the topological
information is taken from the .tpr file anyway. Gromacs may spit out
broken molecules, and will swallow them just as well.

Groetjes,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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The Netherlands
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Re: [gmx-users] Essential dynamics - concepts

[Tsjerk Wassenaar]

Hi Kavya,

On Sat, Jun 4, 2011 at 8:18 AM, Kavyashree M  wrote:
> Dear Gromacs users,
>
>  I am new to essential dynamics, I have gone through
> some fundamentals in PCS, the mailing list related to ED
> and few publications by -
> Amadei (Proteins, 17, 412-425, 1993),
> a. Amadei (journal of biomolecular structure and dynamics, 13, 615, 1996)
> b. Berk Hess (Physical reviews E, 62, 8428-8448, 2000)
> c. Berk Hess (Physical reviews E, 63, 031910, 2002)
> d. Caterina (Biophysical chemistry, 92, 183-199, 2001)
>
> I have made a short note of what I understand. Please correct.
> the mistakes.
> 1. ED is principally used to study the anharmonic motions, ie those
>    which are not equilibrated unlike equlibrated motions like bond
>    vibrations, bending etc.. (Equilibrated in the time scale of study)

No, ED does not make any assumptions on the nature of motions. It does
not distinguish anharmonic from harmonic motions. It also does not
distinguish between equilibrated and non-equilibrated motions. It will
give insight in correlated (global) and non-correlated (local)
motions. Note that it will only give linearly correlated motions, and
neglects non-linear correlations. Also note that it will not give the
motions that are most strongly correlated, btu those which have the
largest extent of motion, collectivelye. (There is a modification on
the gromacs contribution page to give the motions of highest
correlation.

> 2. So one has to run a simulation long enough so that it is more than
>    or equal to the time scale required for the specific motion (for eg.
>    closing of loop takes place in few ps, one has to run MD for atleast
>    a ns to investigate it)

PCA/ED only allows one to make statements about the time scales
simulated, so to describe a certain motion, the simulation has to be
long enough to encompass the motion.

> 3. After MD for long enough time, when covariance matrix would indicate
>    whether two atoms move in same direction, or opposite over the time
>    of simulation based on positive or negative value. Extracting Eigenvalues
>    and Eigenvectors from the matix gives the directions in which the highly
>    correlated motions occur.

The eigenvectors give the direction of the motion in conformational
space, and the the eigenvalues the associated extents of the motions.
An eigenvalue is an RMSF of the collective motion.

> 4. Analysing all the data values projected over the first few eigen vectors
>     is the priciple component analysis.

No, 'Principal component analysis' is rewriting the original data with
many variables as a set of new variables that are linear combinations
of the original ones but describe the underlying structure better.
These new variables, the principal components or latent variables,
presumably reflect the true degrees of freedom better.

> 5. if this experiment is done on same structure more than once (say 3), and
> the first few priciple components of all 3 simulations coincide, then it
> could be
>     the most possible direction of motion in the protein otherwise the
> patern
>     of PC's is most likely due to random motion.

No, if they do not agree, then probably your system is ill-converged.
But that is not the same as being random.

> My questions -

> 1. While chosing the period for covariance analysis, what is the criteria?
> in the
>     paper b, author mention that a certain peroid was chosen because the
> peptide
>     free enegry minimum. Not clear about this, because when the protein
> resides in
>     an energy minimum how can there be transition to another configuration
> (eg a loop
>     movement) without crossing the barrier. should we not consider the time
> which
>     spans a native conformation to say an active conformation during the
> simulation?

It depends on the time required for equilibration and the time scale
of the process you're interested in. There's no golden standard there.

> 2. If we have done a long enough simulation of say 100ns for 4 proteins with
> similar
>    structure but with sequence id of 40-60% (different chain lengths
> 230-260aa), Can
>    we do a covar analysis of these 4 simulations?

You can always do covariance analysis. Whether it makes sense is the
real question ;) But it may certainly make sense to do covariance
analysis on related systems.

> 3. How much should be the socine content to tell that it is not a random
> diffusion?

All cows are animals, but not all animals are cows. Likewise, the
principal components of random diffusion are characterised by their
fit to a cosine series, but if you're projections yield a perfect fit
to a cosine series... In most cases such a fit is obtained when the
system is still equilibrating.

> 4. Is ED analysis itself is not enough to establish a important movement in
> the
>     protein.. further ED sampling is required to prove it?

Whether it's important is up to the researcher :)

> 5. Concept doubt - When all the structures at least square fitted before
> building 

Re: [gmx-users] Essential dynamics - concepts

[Tsjerk Wassenaar]

Hi Kavya,

> Its g_covar contributed by Dr. Rossen apostolov if I am right.  Here it
> states that those which are having correlation coefficient better than 0.5
> will be reported, so covariance gives those which have correlation
> coefficient
> less than 0.5?

I don't know the modified version. But I presume that the components
with eigenvalues higher than 0.5 are written out, which is not quite
the same as having a correlation coefficient of 0.5.

> So here the criteria for ill-convergence is the disagreement in
> the principle
> components of the 3 simulations, while random diffusion is the inherent
> property of PCA and its only the extent to which it can be fitted to a
> cosine
> that distinguishes if from a true random motion and any meaningful
> correlations.

Please get the random diffusion out of your head! :p
Also, do some more background reading on PCA as a
mathematical/statistical technique, not in relation to molecular
simulations. It helps to form a better view on the matter.

> I understand here that time depends on the system under consideration. But
> my doubt was - for example if we consider a situation where time required
> for
> a conformational change of a protein from native to an active state is
> 100ps,
> then we run a simulation for some 5ns, so theoretically this change of
> conformations
> should have taken place 50 times in that 5ns time span. So if we take any
> 100ps
> (or to be on the safer side 500ps) time for the covariance analysis, after
> the system
> has equilibrated ie., leaving first few hundred ps, then we will be able to
> capture
> this feature of correlated movement in the covariance analysis, is that
> right?

Most proteins will take quite a bit longer than 100ps to go from one
to the other state. But besides that, if on average a process takes a
certain time, it is not said that an interval of that length (or twice
that length) will also contain the transition. You should have
additional measures for the state of the protein and can then use PCA
to understand which collective motions are related to the transition.

> In this case should we merge all the .xtc files and superpose all the
> conformations
> with a single pdb file. and then do a covar analysis? Will the difference in
> the amino acid
> and the length of the sequences matter during covariance analysis when we
> deal
> with structures with different sequence but with high degree of structural
> similarity?

You can merge them. It's not the only way though, but I think it goes
to far to try and explain the ins and outs here :p Do mind that any
systems you want to compare have to have the same conformational
space! In casu, that means that you have to extract trajectories of
those parts of the system that are common to all variants.

> Any numerical measure of the value of cosine content beyond which the
> analysis is said
> to be more of a random nature than being meaningful?

It's not about randomness!

> So in the paper, Berk Hess (Physical reviews E, 62, 8428-8448, 2000), an
> experiment
> conducted on Ompf porin, why is there a cosine nature in first four PC's,
> indicative of
> randomness, even when they have least-square fitted the structures before
> covariance
> analysis?
> Its quite unclear for me Sir as to what physically it means to say that
> there is random
> diffusion even after least-square fitting?

If the scores (the projection of the trajectory) on the first
principal component fit a cosine, it is indicative of a unidirectional
process. Random diffusion of an atomic system is a unidirectional
process.

Note I'm not going to reply on covariance analysis more today :) Just
be sure to take some time to think things over. Read a bit more from
alternative sources, and let it all diffuse randomly into your head...
:p

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Essential dynamics - concepts

[Tsjerk Wassenaar]

Hi Kavya,

> Thanks sir. I will go through them. However I have referred -
> "A Tutorial on Principle component Analysis" by  Lindsay I Smith.
> Which gave a good understanding about the concepts. Still I
> have some doubts regarding eigen values, as you have told
> I will think over them again.

I know that one :) I'd advise others thinking of using PCA in MD to
also read it...  It also pays off to read a few more, though, to get
slightly different viewing angles and to get used to different ways of
telling the same story.

> But one statement I was not clear from your previous mail  that -
> "An eigenvalue is an RMSF of the collective motion."

I shouldn't have said RMSF, as it's not the root. The first eigenvalue
is the variance or mean square fluctuation of the projection of your
data onto the first eigenvector.

>
> These eigenvalues are the solutions for an Nth order equation
> arising from N X N covar (sorry for using this term again) matrix
> (considering only x component). If we consider this covar matrix
> as a transformation matrix, eigen value would give the magnitude
> and direction by which the eigenvector is transformed linearly.
> Is it correct?

No, the matrix of eigenvectors is a transformation (rotation) matrix.
The eigenvectors in a sense give the directions of motion, and the
eigenvalues the magnitudes.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] ED-analysis

[Tsjerk Wassenaar]

Hi Kavya,

> 1.  Can the .xtc file from MD be used directly for analysis
>  without applying -pbc nojump or mol option? [I had
>  asked the same question before but was not clear
>  with the answer.

It is absolutely necessary that the molecules be whole, and in the
case of multimers, correctly assembled.
>
> 2.  While calculating the RMSIP (root mean square inner
>     product) suppose the 10 eigen vectors in one simulation
>     is not in the same order as in the second simulation ie.,
>     the first ranked eigen vector in one simulation is equivalent
>     to second ranked eigen vector in another simulation
>     being compared - How can this ambiguity be taken care of?

Worse, the first eigenvector can be dispersed over the second and
third in another (equivalent) system. But this is what the RMSIP is
for. It is a measure to indicate how much one set of eigenvectors
corresponds to another, regardless of the order.

> 3. Before comparing two ED simulations is it required to align
>     all the structures to only one initial structure? As the orientation
>     of the two initial structures may differ?

Yes, it is absolutely necessary that the conformational space is
defined in the same way for the different systems. Let's say you have
a set of configurations X, for which you determine the covariance
matrix and the eigenvectors/-values:

S = (1/N)XX' = PDP'

Now take the same system, but rotated:

T = (1/N)RXX'R' = RPDP'R'

So the eigenvectors for the rotated configurations are rotated too.

> 4. Kindly provide a clear protocol for the essential dynamics
>     analysis of 4 proteins with different sequence length and
>     sequence similarity. but the native structures superpose
>     very well 3 dimensionally.

This is up to you... Sorry.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] ED-analysis

[Tsjerk Wassenaar]

Hi Kavya,

>> It is absolutely necessary that the molecules be whole, and in the
>> case of multimers, correctly assembled.
>
> But if there is only one polymer (protein) with water in the system
> then also is it necessary to use nojump or mol in trjconv?because
> in one of the mails -
>
> http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html
>
> there was a discussion regarding this topic. So I wanted to
> ensure regarding that aspect. Molecule after simulation
> crosses the box boundary in the simulation I have done, So
> if I processed analyzing with the native .xtc file there will be
> a problem? But in this case its a single intact protein molecule
> in water.

That post concerns -pbc nojump. My reply to you was about having
molecules in one piece. They're different things. Gromacs nowadays
doesn't care about molecules being whole in the trajectory file, and
happily writes them in pieces. So you can't be confident you can use
the trajectory as is.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] standard deviation about rmsd and rmsf values

[Tsjerk Wassenaar]

Hey,

The rmsf and rmsd are themselves sort of standard deviations. They are chi
distributed, and the confidence intervals are generally not characterized by
a standard deviation, which would be a standard deviation of a standard
deviation :p

Cheers,

Tsjerk

On Jun 18, 2011 1:21 PM, "Francesco Oteri" 
wrote:

g_analyze -f file.xvg

the program prints, for each data set, the average and standard deviation

Il 18/06/2011 13:18, shahab shariati ha scritto:

> > Dear gromacs users > > I want to know how to obtain standard deviation
about rmsd and rmsf valu...
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Re: [gmx-users] cross correlations

[Tsjerk Wassenaar]

Hey,

The method from Lange is quite a different thing. It includes
non-linear correlations, which is interesting to look at for overall
correlation between atoms. If the ultimate goal is to do PCA on it,
then it will give you awkward components that will give you a hard
time trying to interpret.

There is another way, besides using an external tool. Extract the
diagonal elements and take the square root of each. Then for each
element [i,j] in the matrix, divide by the elements i and j of these
square roots, and you'll have yourself a correlation matrix.

Hope it helps,

Tsjerk

On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov
 wrote:
> Hi.
>
> There is two possibilitys
> 1. utility written by   Oliver F. Lange and Helmut Grubmüller [1] that
> compites
> general corelation coefficients
> 2. My utility that computes pearson correlation coefficients [2]
>
> [1]
> http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html
> [2]
> http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl
>
>
> On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote:
>>
>> Dear all,
>>
>> Is there any built in function that gives me the pairwise correlation
>> of the fluctuation (unit vector between two coordinates of a residue)
>> of residues (averaged over the input trajectory). I tried g_covar but
>> thats not what im looking for. The result I want should be an NxN
>> matrix with values ranging from -1 to 1.
>>
>> Thanks in advance,
>> Nihal
>>
>> --
>> Elif Nihal Korkmaz
>>
>> Research Assistant
>> University of Wisconsin - Biophysics
>> Member of Qiang Cui & Thomas Record Labs
>> 1101 University Ave, Rm. 8359
>>  Madison, WI 53706
>>  Phone:  608-265-3644
>>  Email:   kork...@wisc.edu [1]
>>
>>
>>
>> Links:
>> --
>> [1] mailto:kork...@wisc.edu
>
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Institute, Russia
> Department of Molecular and Radiation Biophysics
> Gentoo Team Ru
> Gentoo Linux Dev
> mailto:alexx...@gmail.com
> mailto:ale...@gentoo.org
> mailto:ale...@omrb.pnpi.spb.ru
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] cross correlations

[Tsjerk Wassenaar]

Of course you did... Though mind the brackets :)

C_ij =  / sqrt (  *  )

The point I want to make is that you can easily take the output from
g_covar -ascii and turn it into a correlation matrix. In R
(r-project.org) there is even a dedicated function for it:

x <- scan("covar.dat")
x <- matrix(x,sqrt(length(x)))
y <- cov2cor(x)
write(y,"correl.dat",ncolumns=3)

Cheers,

Tsjerk

On Sun, Jun 19, 2011 at 12:37 PM, Alexey Shvetsov
 wrote:
> Hi,
>
> Thats actualy that i did here [1]. Extracting coordinate for every atom in
> interesting two group and computing
>
> C_ij =  / sqrt ( x_i ^2 * x_j^2 ) assuming that x_i and x_j is
> vectors
>
>
> [1]
> http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl
> On Sun, 19 Jun 2011 12:27:53 +0200, Tsjerk Wassenaar wrote:
>>
>> Hey,
>>
>> The method from Lange is quite a different thing. It includes
>> non-linear correlations, which is interesting to look at for overall
>> correlation between atoms. If the ultimate goal is to do PCA on it,
>> then it will give you awkward components that will give you a hard
>> time trying to interpret.
>>
>> There is another way, besides using an external tool. Extract the
>> diagonal elements and take the square root of each. Then for each
>> element [i,j] in the matrix, divide by the elements i and j of these
>> square roots, and you'll have yourself a correlation matrix.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>> On Sun, Jun 19, 2011 at 11:55 AM, Alexey Shvetsov
>>  wrote:
>>>
>>> Hi.
>>>
>>> There is two possibilitys
>>> 1. utility written by   Oliver F. Lange and Helmut Grubmüller [1] that
>>> compites
>>> general corelation coefficients
>>> 2. My utility that computes pearson correlation coefficients [2]
>>>
>>> [1]
>>>
>>>
>>> http://www.mpibpc.mpg.de/home/grubmueller/downloads/GeneralizedCorrelations/index.html
>>> [2]
>>>
>>>
>>> http://omrb.pnpi.spb.ru/gitweb/?p=gromacs/gromacs.git;a=shortlog;h=refs/heads/alexxy/g_correl
>>>
>>>
>>> On Fri, 17 Jun 2011 00:48:01 -0500, E. Nihal Korkmaz wrote:
>>>>
>>>> Dear all,
>>>>
>>>> Is there any built in function that gives me the pairwise correlation
>>>> of the fluctuation (unit vector between two coordinates of a residue)
>>>> of residues (averaged over the input trajectory). I tried g_covar but
>>>> thats not what im looking for. The result I want should be an NxN
>>>> matrix with values ranging from -1 to 1.
>>>>
>>>> Thanks in advance,
>>>> Nihal
>>>>
>>>> --
>>>> Elif Nihal Korkmaz
>>>>
>>>> Research Assistant
>>>> University of Wisconsin - Biophysics
>>>> Member of Qiang Cui & Thomas Record Labs
>>>> 1101 University Ave, Rm. 8359
>>>>  Madison, WI 53706
>>>>  Phone:  608-265-3644
>>>>  Email:   kork...@wisc.edu [1]
>>>>
>>>>
>>>>
>>>> Links:
>>>> --
>>>> [1] mailto:kork...@wisc.edu
>>>
>>> --
>>> Best Regards,
>>> Alexey 'Alexxy' Shvetsov
>>> Petersburg Nuclear Physics Institute, Russia
>>> Department of Molecular and Radiation Biophysics
>>> Gentoo Team Ru
>>> Gentoo Linux Dev
>>> mailto:alexx...@gmail.com
>>> mailto:ale...@gentoo.org
>>> mailto:ale...@omrb.pnpi.spb.ru
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface
>>> or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Institute, Russia
> Department of Molecular and Radiation Biophysics
> Gentoo Team Ru
> Gentoo Linux Dev
>

Re: [gmx-users] radius of gyration - compactness

[Tsjerk Wassenaar]

Hey Shahab,

What's the contradiction?

> [ Furthermore, INT–DBD appears less compact in the complex, as far as the
> radius of gyration increases and more molecular surface is exposed to the
> solvent (Table 1). ]

larger radius of gyration, less compact, more surface

> [ Furthermore, according to radiuses of gyration of two proteins in the two
> systems, the protein in the complex is more
> compact than the free protein, this is consistent with the result of
> structure stability comparing. It means that less
> molecular surface of homeodomain protein in the protein– DNA complex is
> exposed to the solvent.]

(smaller radius of gyration; not stated explicitly), more compact, less surface.

Seems consistent to me...

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] adius of gyration - compactness

[Tsjerk Wassenaar]

Hi Shahab,

> I want to know exactly how do radius of gyration of protein from free state
> to complex state change .
> Rg increased od decreased?

That depends on the protein. Some will, e.g., close or fold upon
binding, while others may open up, or unfold.

> I want to know my data [ In my simulation systems, the average of radius of
> gyration in free protein
> is 2.31 and for protein in complex is 2.58.] is true?

It's true, because you found it. Whether it correctly reflects the
state of the system you're after depends on the quality of your model,
the time scale simulated and the tims scale of conformational changes
involved in (un)binding. There's no rule of thumb.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] radius of gyration - compactness - accessible surface area

[Tsjerk Wassenaar]

Hi Shahab,

When comparing two variables, they have to share an axis. Time for instance...

Cheers,

Tsjerk

On Tue, Jun 21, 2011 at 6:36 AM, shahab shariati
 wrote:
> Dear Tsjerk
>
> thanks for your attention.
>
>  larger radius of gyration, more surface. and smaller radius of
> gyration, less surface.
>
> I want to obtain solvent accessible surface area using g_sas.
>
>
> g_sas -f *.xtc -s *.tpr -n *.ndx -o -or -oa.
>
> I will obtain three output files containing: area.xvg, resarea.xvg and
> atomarea.xvg
>
> If I want to obtain average of ASA  to compare with Rg (I want to know
>
> in my system, with increase of Rg, how do ASA
> change?), which of above output files are suitable for this aim?
>
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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Re: [gmx-users] radius of gyration - compactness - accessible surface area

[Tsjerk Wassenaar]

You understand correctly.

On Tue, Jun 21, 2011 at 11:35 AM, shahab shariati
 wrote:
> Dear Tsjerk
>
> very thanks for your useful guidance.
>
> I now know that I should compare output of g_gyrate (containing Rg vs time)
> by area.xvg output file of g_sas (containing area vs time).
>
> In area.xvg output file, there are several columns: "Hydrophobic",
> "Hydrophilic" and "Total".
>
> for example in time, 100 ps:
>
> 100    35.9501 60.9389 96.8891
>
> area is in nm2.
>
> from above number I understand that 35.9501 nm2 of area of protein that is
> accessible to solvent belongs to
> hydrophobic part of protein.
>
> and 60.9389 nm2 of area of protein that is accessible to solvent belongs to
> hydrophilic part of protein.
>
> is my understanding true?
>
> any help will highly appreciated.
>
>
>
> --
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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Re: [gmx-users] Re: Trajectory and ED - (not old question again)

[Tsjerk Wassenaar]

trjconv -fit rot+trans

Cheers,

Tsjerk

On Jun 23, 2011 8:12 AM, "Kavyashree M"  wrote:

Dear Users,

Are there any tool for superposing the trajectory
structures form MD. Please correct me if I am asking
any illogical question.
My previous question was regarding the trjconv output
pdb trajectory, is there a way to superpose all these
structures?

Thank you
With regards
M. Kavyashree

On Wed, Jun 22, 2011 at 10:52 PM, Kavyashree M  wrote: >
> Dear users, > >I...

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Re: [gmx-users] Re: Trajectory and ED - (not old question again)

[Tsjerk Wassenaar]

Hi Kavya,

For us to say anything sensible about it, we should at least know
exactly what you've tried. Copy-paste the commands exactly as you
issued them, and provide the parts of the output that seem relevant.

Cheers,

Tsjerk

On Thu, Jun 23, 2011 at 9:54 AM, Kavyashree M  wrote:
> Dear Sir,
>
> I tried fitting the proteins of the trajectory in pymol
> as mentioned in your (Dr. Tsjerk's) tutorial, but later
> I tried using the trjconv -fit rot+trans to fit the proteins
> in the trajectory as you had mentioned.
>
> I do not observe this degree of movement in protein
> when I view the trajectory along any 1-5 eigen vectors.
> This trajectory along any of these eigen vector is very minute
> and cannot be compared to that obtained after superposing
> the structure in the trajectory. Why is it so?
> Please let me know if I am understanding the concept wrong.
>
> Thanking you
> With regards
> M. Kavyashree
>
>
> On Thu, Jun 23, 2011 at 11:56 AM, Kavyashree M  wrote:
>>
>> Thank you Sir!
>>
>> With regards
>> M. Kavyashree
>>
>> On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar 
>> wrote:
>>>
>>> trjconv -fit rot+trans
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Jun 23, 2011 8:12 AM, "Kavyashree M"  wrote:
>>>
>>> Dear Users,
>>>
>>> Are there any tool for superposing the trajectory
>>> structures form MD. Please correct me if I am asking
>>> any illogical question.
>>> My previous question was regarding the trjconv output
>>> pdb trajectory, is there a way to superpose all these
>>> structures?
>>>
>>> Thank you
>>> With regards
>>> M. Kavyashree
>>>
>>> On Wed, Jun 22, 2011 at 10:52 PM, Kavyashree M  wrote:
>>> > > Dear users, > >    I...
>>>
>>> --
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>>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Re: Trajectory and ED - (not old question again)

[Tsjerk Wassenaar]

Hi Kavya,

For certain I do not state in my tutorial that one should use g_nmtraj
for this. It is intended for analysis of normal modes analysis, where
the eigenvalues are related to the frequencies of the harmonic
motions. You're using it on the modes with largest eigenvalues, which
are interpreted as high frequencies, consequently giving small
amplitudes. This explains that you're not seeing much.

To get an idea of the extent of the motion, look at the extreme
projections. To see how the trajectory moves along a certain mode, use
g_anaeig -filt

Cheers,

Tsjerk

On Thu, Jun 23, 2011 at 10:56 AM, Kavyashree M  wrote:
> Dear Sir,
>
> 1 simulation for 100ns -
> ED analysis proceeded as follows:
>
> g_covar -s .tpr -f ..xtc -o eigenvectors.xvg -v
> eigenvalues.trr -xpma covar.xpm
> g_anaeig -s .tpr -f .xtc -v eigenvectors.trr -eig
> eigenvalues.xvg -proj proj-evi.xvg -extr evi.pdb -rmsf rmsf-evi.xvg -first i
> -last i
> (here i refers to the eigen vector index)
> Thus generated 5 eigen vectors.
>
> Visualised the trajectory along these eigen vectors using
>
> g_nmtraj -s tpr -v eigenvector.trr -o pdb -eigen i  -phases x
> -temp x -amplitude x -nframes x
> (i referes to eigen vectors. In this I was not clear about the significance
> of phases, amplitude)
>
> I visualised the pbd output in pymol there was very minute movement of some
> loop regions.
>
> on the other side-
> When I visualised the .xt file output as pdb according to  Dr.Tjerk's
> tutorial or
> by superposing all the structures in trajectory over initial structure in
> pymol
> there was a significant degree of movement in those loops.
>
> so my question here is why these two does not correlate. I agree that
> trajectory
> along one eigenvector might not give movements of all the regions that is
> observed
> in superposed trajectory but whichever region it shows movements is
> extremely less
> compared to that when viewed from superposed structures in trajectory.
>
> I hope this is not confusing.
>
> Thanking you
> With regards
> M, Kavyashree
>
> On Thu, Jun 23, 2011 at 1:27 PM, Tsjerk Wassenaar  wrote:
>>
>> Hi Kavya,
>>
>> For us to say anything sensible about it, we should at least know
>> exactly what you've tried. Copy-paste the commands exactly as you
>> issued them, and provide the parts of the output that seem relevant.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Jun 23, 2011 at 9:54 AM, Kavyashree M  wrote:
>> > Dear Sir,
>> >
>> > I tried fitting the proteins of the trajectory in pymol
>> > as mentioned in your (Dr. Tsjerk's) tutorial, but later
>> > I tried using the trjconv -fit rot+trans to fit the proteins
>> > in the trajectory as you had mentioned.
>> >
>> > I do not observe this degree of movement in protein
>> > when I view the trajectory along any 1-5 eigen vectors.
>> > This trajectory along any of these eigen vector is very minute
>> > and cannot be compared to that obtained after superposing
>> > the structure in the trajectory. Why is it so?
>> > Please let me know if I am understanding the concept wrong.
>> >
>> > Thanking you
>> > With regards
>> > M. Kavyashree
>> >
>> >
>> > On Thu, Jun 23, 2011 at 11:56 AM, Kavyashree M 
>> > wrote:
>> >>
>> >> Thank you Sir!
>> >>
>> >> With regards
>> >> M. Kavyashree
>> >>
>> >> On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar 
>> >> wrote:
>> >>>
>> >>> trjconv -fit rot+trans
>> >>>
>> >>> Cheers,
>> >>>
>> >>> Tsjerk
>> >>>
>> >>> On Jun 23, 2011 8:12 AM, "Kavyashree M"  wrote:
>> >>>
>> >>> Dear Users,
>> >>>
>> >>> Are there any tool for superposing the trajectory
>> >>> structures form MD. Please correct me if I am asking
>> >>> any illogical question.
>> >>> My previous question was regarding the trjconv output
>> >>> pdb trajectory, is there a way to superpose all these
>> >>> structures?
>> >>>
>> >>> Thank you
>> >>> With regards
>> >>> M. Kavyashree
>> >>>
>> >>> On Wed, Jun 22, 2011 at 10:52 PM, Kavyashree M 
>> >>> wrote:
>> >>> > > Dear users, > >    I...
>> >>>
>> >>> --
>> >>> gmx-users mailing list    gmx-users@gromac

Re: [gmx-users] cross correlations

[Tsjerk Wassenaar]

Hi Bipin,

Read them in as a vector of numbers and divide them into sqrt(len(vector))
rows to get yourself a nice square correlation matrix.

Cheers,

Tsjerk

On Jun 24, 2011 3:28 PM, "bipin singh"  wrote:

Hello,
I have some doubts regarding the output file correl.dat as it contains 3
columns, but I am not able to get what are
these column contains,I mean how to change it to the format in which I can
directly plot the data to get DCCM map...
For e.g in this form
Res1  Res2  Correlation coefficient
x yz

On Sun, Jun 19, 2011 at 16:16, Tsjerk Wassenaar  wrote: >
> Of course you did..
---
*Regards,*
Bipin Singh


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Re: [gmx-users] ED - Projecting on an eigenvector

[Tsjerk Wassenaar]

Did you make the molecules whole and removed jumps (in case of a multimer)
prior to filtering?

Cheers,

Tsjerk

On Jun 24, 2011 8:10 PM, "Kavyashree M"  wrote:

Dear user,

When projection of a trajectory (50ns) on an eigen vector
was visualised in pymol, there was broken chains, but when
I projected the simulation (continued for 50 more ns ie.,
total 100ns) this broken chain was not seen why?

Thanking you
With Regards
M. Kavyashree

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Re: [gmx-users] cross correlations

[Tsjerk Wassenaar]

Hi Bipin,

You have three coordinates per residue, hence a 3Nx3N matrix.

Cheers,

Tsjerk

On Jun 25, 2011 4:40 PM, "bipin singh"  wrote:

Hello,
I have calculated the covariance matrix for C-alpha atoms(179 aa) only,but
after plotting the correlation, I have observed that it is
 of 537X537,instead of179X179.Please suggest me how to get correlation
between the C-alpha atoms only.

On Fri, Jun 24, 2011 at 22:54, Tsjerk Wassenaar  wrote: >
> Hi Bipin, > > Read...
-- 
---
*Regards,*
Bipin Singh


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Re: [gmx-users] Periodic Images - clarification

[Tsjerk Wassenaar]

Hey,

Maybe I missed this, but what type of unit cell did you use? You
should use a rhombic dodecahedron.

Then, I would argue that it isn't necessarily so problematic as the
others put it when you have transient contacts. For the greater part
of the simulation the distances in the periodic system are so large
that there can be no direct effect between opposite ends of the
protein. It is unlikely that the brief periods where the opposite ends
were within each others sphere of influence - not in contact - would
have caused a persistent deviation from in ensemble. Mind that it's
not wrong that a protein would suddenly feel some presence from some
end of a similar protein some distance away at some time. It's just
wrong if a protein aligns with itself. That has not happened if these
minimal distances were only transient. It may well be that the protein
was going from one conformation to another, for which it had to go
through something that would violate the PBC a bit. Still, you are in
for some discussion, and have to argue, based on what the simulation
shows you, what (a) replicate simulation(s) show(s) you and what you
know of your protein, why it would be justified to draw conclusions
based on that trajectory.

But those are just my two cents.

Cheers,

Tsjerk

On Sun, Jun 26, 2011 at 5:41 PM, Justin A. Lemkul  wrote:
>
>
> Kavyashree M wrote:
>>
>> Sir,
>>  I would like to thank you for patiently replying for my repeatedly asked
>> question.
>>
>>
>>    For most stable, well-behaved proteins, setting a suitable box size
>>    at the outset of the simulation is sufficient to avoid spurious PBC
>>    interactions.  In your case, there are several possibilities: (1)
>>    the protein is not well-behaved, (2) you didn't set the box you
>>    think you did, (3) the .mdp settings are wrong and lead to
>>    instability, or (4) your pressure coupling settings cause the box to
>>    shrink unreasonably.
>>
>>  1. protein is not well behaved - This point I dont know how to quantify.
>
> It's not necessarily something you can quantify, it's more of a qualitative
> measure in many cases and comes from anticipating what the system may do.
>  Not all proteins are stably folded.  Some may unfold, others may have
> multiple domains that will move along hinge regions, causing the protein to
> expand its size, etc.  The initial box size assumes that large changes in
> the structure will not occur.  Sometimes this assumption is not good.
>
>> 2. Box dimensions - I repeated from the model, editconf gave the same box
>> dimensions which I had used earlier but did not      repeat the NVT. and the
>> distance -d between wall of box and protein atom was kept as 1.0nm while the
>> max cut of used was
>>   1.4nm.
>> 3. I am attaching the mdp file.
>> 4. I checked the whole trajectory for change in box size with the output
>> of g_energy. But did not find and abrupt deviations
>>
>
> OK.
>
>>
>>    If you want to use the first 26 ns only, I suppose these data are
>>    legitimate, although then several questions arise.  Why did you run
>>    100 ns in the first place?  Presumably you felt that you needed such
>>    a simulation length to address whatever question you're asking, so
>>    is 26 ns legitimate, or is it simply convenient because you don't
>>    want to run the simulation again?  Also, why trust these results
>>    when you know that just a short time later these dynamics produced
>>    flawed information?  The PBC violation may not have simply happened
>>    suddenly; maybe it was a product of some long-term motion in the
>>    system that was continually trending towards disaster.
>>
>>  I did not anticipate such a violation would as it did not happen in other
>> cases. so I did not check the minimum image violation
>> while running the simulation but caculated after 100ns. I agree it was my
>> stupidity. Because of time constraints and system unavailability now I might
>> not be able to run another simulation. But I will be running it later with
>> corrected parameters for sure.
>>
>> I agree that it is producing flawed results. But My point was if at all it
>> was caused only due to the box dimension being smaller
>> and not due to any wrong parameters used why is that 26ns wrong. Probably
>> if I had selected a bigger box size may be that
>> loop would have continued to move without minimum image violation.
>>
>>    The biggest question is, if you run the simulation again (which you
>>    should, but only after answering the four points above and the
>>    following), how do you know the same thing won't happen again?
>>     You've been asking related questions for weeks and I still do not
>>    know if you have followed my repeated advice to watch the trajectory
>>    with a PBC unit cell enabled in your favorite visualization program
>>    and, in concert with the identified problematic atoms in the
>>    g_mindist output, identify where and why the minimum image violation
>>    occurred.  Doing so should take 

Re: [gmx-users] Periodic Images - clarification

[Tsjerk Wassenaar]

Hi Kavya,

> I did use dodecahedron cell.  but how does using a dodecahedron cell
> be advantageous than any other cell when minimum image violation
> has occurred? This is just my inquisitiveness.

In a rectangular cell, such interactions may occur merely by
reorientation of the solute. In that case it is likely that
self-interactions over PBC have a persistent effect on the dynamics.

> And when I was visualizing
> the trajectory in VMD along with other periodic images in +/-X, +/-Y and
> +/-Z
> directions I saw only 26images, this is good for a cubic cell. But how
> can I visualize a dodecahedron cell? Which has more faces ---> more periodic
> images (If I am not wrong) than a cubic or rectangular cell..

Actually, there are less. A rhombic dodecahedron has 12 neighbours. A
cubic/rectangular cell has 6 faces, but for those you also have to
consider the neighbours at the edges and corners, which brings the
total to 26.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] g_msd bug

[Tsjerk Wassenaar]

Hi Slawomir,

That's quite a usage of memory! Can you provide more information? Like
the number of frames in the trajectory, the command line you used, and
the system you ran on?

Cheers,

Tsjerk

2011/6/27 Sławomir Stachura :
> Hi GMX Users,
> I am writting this email, beacause I think the g_msd program in Gromacs 4.5.4 
> bears a problem. I was calculating the MSD od center of mass of POPC in 
> membrane (system contains 274 POPC lipid molecules in all-atom force field) 
> from 50 ns trajectory and it seems to consume great amount of memory. With  
> time of calculations the memory reserves are gradually devoured to the 
> extent, in my case,  of over 600 GB (than my administrator of cluster killed 
> the process). It seems that it does not release memory and it's pilling 
> results up with steps  in memory. Have you heard of such case?
> Best wishes,
>   Slawomir--
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] about periodic images violation

[Tsjerk Wassenaar]

Hi Anna,

The spikes you see occur because the protein is broken over the
periodic boundaries. Not hard to see that a broken molecule will have
a minimal minimal distance.

The other problem may well occur due to rotation of your molecule.
Since you set -bt tric, you just get a rectangular unit cell, which
has the drawback that the shortest distance may not be long enough to
keep the protein from self-interactions in certain orientations. I
know it's considered a pretty standard setup, which is why I mentioned
it before. You should use a rhombic dodecahedron.

With a rectangular cell, you could even have self-interaction in a
nastier way: the ends of the protein can try to avoid each other,
rather than align with each other. That would result in an altered
ensemble, yet one in which you wouldn't see violations of the minimal
distance. In a rhombic dodecahedron the spatial distribution is much
more uniform...

Cheers,

Tsjerk

On Mon, Jun 27, 2011 at 12:48 PM, Anna Marabotti
 wrote:
> Dear gmx-users,
> I'm inserting into the discussion about periodic images since I'm
> experimenting a problem of minimum distance violation too. I'm doing
> simulations on a dimeric protein (with no covalent bonds between the two
> subunits) which derives not from a crystallographic structure but from a
> model. I made several simulations changing the gen_seed in order to explore
> deeply the conformational space of the protein. I used a triclinic box
> (option editconf -bt triclinic -d 1 -c) filled with spc water and
> neutralized with ions; in my opinion, it's quite a standard system. I
> equilibrated the system with a minimization (emtol = 500 reached) and with
> NVT+NPT in position-restrained mode (20+100 ps) at 310 K, then launched the
> full MD for 30 ns, always at 310 K. I repeated this procedure
> (NVT+NPT+FullMD) for each of the gen_seed assigned (random numbers),
> starting from the same minimized structure. Obviously, in PR-NPT and full Md
> simulations, I did not recalculated the initial velocity (it's a
> continuation). Before starting with full MD I checked for energetic
> parameters in .edr file (Pot, Kin, Tot, T, P) and all seem stable with no
> apparent problems. I run the 30 ns simulations and now I'm checking for the
> results.
> Looking at the trajectories I see that in some (but not all) cases, the
> protein moves from the center of the box to one of the edges, starting from
> a time that is different in each simulation, when it happens. I run
> g_mindist, and in some cases (generally when the protein doesn't move so
> much) I see some "spikes" in the plot (that disappear if I apply trjconv
> -pbc nojump to the trajectory), but apart from these "spikes" the minimum
> periodic distance in the trajectory is at least 1.5 nm (I set van der Waals
> cut-off at 1.4 nm). In other cases, however (essentially when the protein
> starts moving towards the edges of the box), the minimum periodic distance
> starts decreasing (in some simulations after 10 ns, in some simulations
> after 20: there is not a common point after which you can see a sudden
> decrease of minimum periodic distance of the system) and reaches a value
> below 1.4 nm or even below 1 nm. Considering that the starting system is
> more or less the same in all cases, I don't identify the reason why the
> system "behaves" like this, and moreover what can I do to avoid this. My
> questions are:
> - do I have to enlarge the box? but I don't think that this would solve the
> "motion" of the protein towards one edge of the box
> - do I have to change the box? In his last message Tsjerk suggests to use a
> rhombic dodecahedron box, could it be useful in my case?
> - do you think it's a problem of stabilization of the system? Should I run a
> deeper minimization, or a longer NVT+NPT in my system?
> I'm quite puzzled especially because the system is the same in all cases,
> the only thing I changed in my simulations is the gen_seed.
> Could anybody give me some suggestions about it?
> Thank you very much
> Anna
>
>
>
>
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Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
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Re: [gmx-users] micelle clustering

[Tsjerk Wassenaar]

Hi Sulatha,

Did you install gromacs yourself or are you using a system wide
installation?

A. I installed myself

In that case you go into the directory where you have put the gromacs source
code and put the modified version of gmx_trjconv.c in the subdirectory
src/tools. Then you go into that directory and type 'make trjconv'

B. I just used what was available already

If you're good friends with the system administrator you can ask him/her to
compile the modified trjconv, as under A.
Otherwise, you'd better install gromacs yourself as explained on the gromacs
site and then go to A.

Hope it helps,

Tsjerk

On Thu, Jun 30, 2011 at 10:10 AM, gregory megariotis
wrote:

> Dear Sulatha,
>
> You can try the command trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002with 
> GROMACS 4.5.4.
>
> Best regrds
>
> Grigoris
>
> --- Στις *Πέμ., 30/06/11, ο/η sulatha M. S * έγραψε:
>
>
> Από: sulatha M. S 
> Θέμα: [gmx-users] micelle clustering
> Προς: "Discussion list for GROMACS users" 
> Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18
>
>
> Hi all,
>
> I have simulated a system of randomly dispersed surfactants in water using
> gromacs (4.0.7) for about 100 ns MD. Micelles are formed after around 40 ns.
>  I am using a time step of 0.002 fs with xtc files written every 500
> steps. For analyzing the micellar properties, I tried the commands given in
>
> http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering
>
> and also looked at the various posts given on this topic, (specifically
> Chris Neale's and Tsjerk's mails).
>
> As posted by Chris Neale, I tried using the commands,
>
> 1. trjconv -f a.xtc -o b.gro -pbc cluster -e 0.001 (make sure to just
>
> get one frame)
>
> 2. grompp -f a.mdp -c b.gro -p a.top -o b.tpr
>
> 3. trjconv -f a.xtc -o b.xtc -s b.tpr -pbc nojump
>
>
>
> Also mentioned in Tsjerk' post that
>
> "When doing so, be sure to use a frame which is close enough to the
>
> starting frame in terms of the coordinates. -pbc nojump works based on
>
> the coordinates and if you use a reference which doesn't match the
>
> starting frame close enough everything can get really messed up".
>
>
>
>
>
> I tried the command 1 with
>
>  trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002
>
> and also
>
>  trjconv -f a.xtc -o b.gro -pbc cluster -dump X (where x=2, 4, 6, 8 etc..)
>
> The program gets into a never ending loop.
>
> I also tried the command 1 on a later part of the trajectory (after 40 ns),
> there also the program enters in a indefinite loop.
>
> I will greatly appreciate any help on how to go about doing this
> specifically which frame (for dump or -e argument) .  Please guide me on
> this.
>
> I also downloaded the modified trjconv.c  by Tsjerk (in one of his posts
> on micelle clustering), but do not know where to incorporate this. I need
> some help on how to use this modified trjconv code.
>
>
> Thanks for any help or clue,
>
> Sulatha
>
>
>
> -Ακολουθεί συνημμένο-
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] pdb2gmx

[Tsjerk Wassenaar]

Hi Simon,

pdb2gmx takesthe first structure. Taking an average would ba awkward, as it
is unlikely to correspond to a real structure.

Cheers,

Tsjerk

On Jun 30, 2011 6:02 PM, "simon sham"  wrote:

Hi,
I have a question about pdb2gmx. If a pdb file contains a multiple
structures, will it average the coordinates or just pick one of the
structures to convert?

Thanks for your insight.

Simon

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Re: [gmx-users] micelle clustering

[Tsjerk Wassenaar]

Hi Sulatha,

With my clustering algorithm there can be no infinite loop :)
By the way, sorry for the error messages you ran into with compiling
4.0.7. It had escaped me that these changes were made after that
version.

Cheers,

Tsjerk

On Fri, Jul 1, 2011 at 8:29 AM, sulatha M. S  wrote:
> Thanks Mark,
> I will do the analysis in 4.5.4. Hope while doing the micelle clustering I
> will not get into a infinite loop as in 4.0.7.
> If I understand correctly, While using trjconv -pbc cluster,  I should use
> -e 0.002  or the frames (-dump option) in the xtc file  (generated after the
> micelles are formed)
>
> Sulatha
>
>
> 2011/7/1 Mark Abraham 
>>
>> On 1/07/2011 3:35 PM, sulatha M. S wrote:
>>>
>>> Hi Tsjerk,
>>>
>>> I installed gromacs myself. I put the modified gmx_trjconv.c code in the
>>> /src/tools subdirectory where the source code is located and tried the
>>> command
>>> make trjconv
>>> But it gives me a series of error messages, as given below.
>>
>> They're all mismatches because of changes between 4.0.7 and 4.5.4
>>
>>> My gromacs version is 4.0.7. I would like to continue in this version
>>> till I finish the set of runs which I have been doing before moving into
>>> 4.5.4 version. or else can I do the analysis alone in gromacs 4.5.4 with the
>>> xtc files generated from 4.0.7 version?
>>
>> Do that. The file formats are unchanged.
>>
>> Mark
>>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] trjconv keeps asking for tpr

[Tsjerk Wassenaar]

Hi Peter,

The .tpr file is needed for the atom and residue names and numbers.
Coordinates are read from the trajectory.

Cheers,

Tsjerk

On Fri, Jan 6, 2012 at 9:13 AM, Peter C. Lai  wrote:
>
> On 2012-01-06 02:10:49AM -0600, Peter C. Lai wrote:
>> In gromacs 4.5.4, trjconv keeps asking for a .tpr file even for things like
>> -dump. Is this expected? Will it "screw up" the output if I am trying to dump
>> an already modified .xtc (like having used -center)?
> Err, I mean can I give it the .tpr that started the run? Will it still dump
> the recentered trajectory properly?
>
> --
> ==
> Peter C. Lai                    | University of Alabama-Birmingham
> Programmer/Analyst              | KAUL 752A
> Genetics, Div. of Research      | 705 South 20th Street
> p...@uab.edu                     | Birmingham AL 35294-4461
> (205) 690-0808                        |
> ==
>
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-- 
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post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] regarding rmsd and md

[Tsjerk Wassenaar]

Hi Priya,

Inspect your trajectory visually and you'll probably see the cause of the
high RMSD. Also check the mailing list on the topic.

Whether you'll see micelle formation depends on many factors. The time
scale, for example.

Cheers,

Tsjerk

On Jan 7, 2012 7:02 AM, "priya thiyagarajan" 
wrote:

hello sir,

I performed dynamics for my lipopeptide...

After md i thought of calculating rmsd...
i did my md for 4ns..
when i plot graph for rmsd, i got plot til 2.2ns

i dono why it came like this..
can anyone tell me why it is like this..

and also i like to clarify one doubt...

If i do dynamics for 20surfactin, at the end of simulation how my result ll
be..i.e.  whether any  miscelle formation at the end or ll my surfactin ll
be like how it is at the begining..

Thanking you,

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Re: [gmx-users] regarding NVT

[Tsjerk Wassenaar]

Hi Priya,

Does it help if you set

tcoupl = v-rescale

Please read the manual, follow a tutorial properly, and think about what
you're doing and what you get out.

Cheers,

Tsjerk

On Jan 7, 2012 8:54 AM, "priya thiyagarajan" 
wrote:

hello sir,

i followed lysozyme tutorial to do dynamics for my protein..

but at the end of NVT equilibration, my temperature is  at 243K.. but i set
300K to my mdp file ..

mine is not getting equilibrium condition..

 this is my nvt.mdp file


title   =GROMOS43a1 lipopeptide NVT equilibration
define  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator  = md; leap-frog integrator
nsteps  = 10; 2 * 10 = 200 ps
dt  = 0.002 ; 2 fs
; Output control
nstxout = 100   ; save coordinates every 0.2 ps
nstvout = 100   ; save velocities every 0.2 ps
nstenergy   = 100   ; save energies every 0.2 ps
nstlog  = 100   ; update log file every 0.2 ps
; Bond parameters
continuation= no; first dynamics run
constraint_algorithm = lincs; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter  = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid  ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
rcoulomb= 1.0   ; short-range electrostatic cutoff (in nm)
rvdw= 1.0   ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME   ; Particle Mesh Ewald for long-range
electrostatics
pme_order   = 4 ; cubic interpolation
fourierspacing  = 0.16  ; grid spacing for FFT
; Temperature coupling is on
tcoupl  = No; modified Berendsen thermostat
tc-grps = DRG   SOL ; two coupling groups - more accurate
tau_t   = 0.1   0.1 ; time constant, in ps
ref_t   = 300   300 ; reference temperature, one for each
group, in K
; Pressure coupling is off
pcoupl  = no; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz   ; 3-D PBC
; Dispersion correction
DispCorr= EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes   ; assign velocities from Maxwell
distribution
gen_temp= 300   ; temperature for Maxwell distribution
gen_seed= -1; generate a random seed


may i know what is the reason..

initially i did nvt for 100ps but i didnt get equil temperature.
then i increased my time to 200ps.. still i am not getting..




help me with your answer..

Thanking you,
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Re: [gmx-users] how to calculate position displacements ??

[Tsjerk Wassenaar]

Hi Kiwoong Kim,

Check out g_traj

Cheers,

Tsjerk

On Tue, Jan 10, 2012 at 8:09 AM, Kiwoong Kim  wrote:
> Hi.
>
> I have questions about calculating the position change of each particles.
>
> Consider there are 4 atoms diffuses into some channel.
>
> Hence, the aim is to calculate position change (only z-axial direction) of
> each particles (4 atoms) with respect to time.
> I want to keep track of the z-directional position of whole atoms onto same
> graph.
> The x and y - directional position changes can be discarded.
>
> The graph would have to be labeled as following ways:
>
> x-label: time (ps)
> y-label: z (angstrom)
>
> there would be 4 curves (because there exist only 4 atoms for example)
>
> Is there any option to obtain this graph in gromacs???
>
> Thx.
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] multi file input for index files

[Tsjerk Wassenaar]

Hey,

In cases where you do end up with two index files, like resulting from
a script or so, you can also simply combine them by concatenation:

cat A.ndx B.ndx > C.ndx

Of course you'll have to make sure that the group names are unique ;)

Cheers,

Tsjerk

2012/1/10 ahmet yıldırım :
> Thanks Mark and Marzinek,
>
> The Problem is solved:
>
> g_hbond -f traj.xtc -s run.tpr -num AB.xvg -n AB.ndx
>
>> chain A
>
> Found 1234 atoms with chain identifier A
>
>  19 chA :  1234 atoms
>
>> name 19 chainA
>
>
>> chain B
>
> Found 1234 atoms with chain identifier B
>
>  20 chB :  1234 atoms
>
>> name 20 chainB
>
>
>> q
>
>
> 2012/1/10 Marzinek, Jan 
>>
>> So as you can see Gromacs does not support multi file input :) Create one
>> index file and specify there your two groups. Then g_hbond will ask you to
>> choose two groups from this file.
>>
>>
>>
>> Jan
>>
>>
>>
>>
>> ===
>> Jan Marzinek
>> PhD Candidate
>> Centre for Process Systems Engineering
>> Department of Chemical Engineering
>> Imperial College London
>> South Kensington Campus
>> London SW7 2AZ
>> E: j.marzine...@imperial.ac.uk
>> M: +44(0)7411 640 552
>> 
>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
>> behalf of ahmet yıldırım [ahmedo...@gmail.com]
>> Sent: Tuesday, January 10, 2012 8:13 AM
>> To: Discussion list for GROMACS users
>> Subject: [gmx-users] multi file input for index files
>>
>> Dear users,
>>
>> I created two different index files (A.ndx and B.ndx). I want to run the
>> two files at the same time.
>> e.g.
>> g_hbond -f traj.xtc -s run.tpr -num A-B.xvg -n A.ndx -n B.ndx
>> where, I want to calculate the hydrogen bonds between A and B.
>> This command is giving the error as it expected. "Gromacs tools do not
>> support multi file input for index files" from
>> http://sbcb.bioch.ox.ac.uk/users/oliver/software/GromacsWrapper/html/gromacs/core/tools.html.
>> Is this correct? If no, what should I do?
>>
>> Thanks in advance
>> --
>> Ahmet Yıldırım
>>
>>
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>
>
>
>
> --
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>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Coupling groups - Thermostat

[Tsjerk Wassenaar]

Hey,

In addition to the foregoing...
The separate coupling is to prevent draining energy from one part to the
other. It is pretty unlikely that either protein or tube will drain the
other one. Water is always a different story.
You can check the setup you choose afterwards, like after a short run, by
rerunning the sinulation with the split groups and checking the
temperature. E.g. if you run with protein and tube in one group, the should
both end up having the same temperature, within the noise. Do mind the
noise is related to the number of atoms in a group.

Hope it helps,

Tsjerk

On Jan 11, 2012 12:00 AM, "Mark Abraham"  wrote:

On 11/01/2012 6:52 AM, Justin A. Lemkul wrote: > > > > Steven Neumann
wrote: >> >> >> >> On Tue, Jan...
One alternative is to pay attention to the advice at the end of section
3.4.8 of the manual and ref cited there - that separate T-coupling groups
can be worse than the problems they purport to fix.

Mark

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Re: [gmx-users] Coupling groups - Thermostat

[Tsjerk Wassenaar]

Hi Mark,

Please, I did not state that the groups should be coupled separately.
I suggested checking the temperatures of the subgroups of a combined
T-coupling group. So 'moot ..., because T-coupling group ...' is not
really in place.

Cheers,

Tsjerk

On Wed, Jan 11, 2012 at 6:29 AM, Mark Abraham  wrote:
> On 11/01/2012 4:23 PM, Tsjerk Wassenaar wrote:
>
> Hey,
>
> In addition to the foregoing...
> The separate coupling is to prevent draining energy from one part to the
> other. It is pretty unlikely that either protein or tube will drain the
> other one. Water is always a different story.
> You can check the setup you choose afterwards, like after a short run, by
> rerunning the sinulation with the split groups and checking the temperature.
> E.g. if you run with protein and tube in one group, the should both end up
> having the same temperature, within the noise. Do mind the noise is related
> to the number of atoms in a group.
>
>
> Clarifying - the amount of noise is *inversely* related to the number atoms.
> That should be fairly moot, though, because a T-coupling group with less
> than a thousand atoms is probably not worth considering. The algorithms work
> best in macroscopic limits, so a group that's not at least 10% of your
> system is likely not approaching that limit - and grompp will warn you about
> that.
>
> Mark
>
>
> Hope it helps,
>
> Tsjerk
>
> On Jan 11, 2012 12:00 AM, "Mark Abraham"  wrote:
>
> On 11/01/2012 6:52 AM, Justin A. Lemkul wrote: > > > > Steven Neumann wrote:
>>> >> >> >> On Tue, Jan...
>
> One alternative is to pay attention to the advice at the end of section
> 3.4.8 of the manual and ref cited there - that separate T-coupling groups
> can be worse than the problems they purport to fix.
>
> Mark
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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