[gmx-users] Simulation a labeled protein

[Faezeh Nami]

Dear all

I am trying to simulate a protein which a label  (a small organic molecule)
is covalently attached to a cysteine. Worth to say there is no label in the
original pdb file of protein and it was attached to the Cys. using a
software.
Should I insert the label parameters into the conf.gro file or I need to
modify a force field? If there is someone who has experiences in such
systems, please have some advice.

Thanks in advance,
Faezeh
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[gmx-users] Conversion of the GLYCAM dihedral parameters

[sa]

>
> Yeah I have also found this page. Finally I did the conversion. I am
> currently testing the parameters.
>

Thank you  Austin and Mark for your help

SA-

>
> --
>
> Message: 4
> Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT)
> From: "Austin B. Yongye" 
> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
>in the  GROMACS format.
> To: Discussion list for GROMACS users 
> Message-ID:
><1311171438.14853.yahoomailclas...@web161422.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> > So my questions are: how to convert it in the gromacs format ?
> I haven't done AMBER to GROMACS conversions. But a google search led me to
> this page. It's just a matter of knowing the different formats.
>
> http://ffamber.cnsm.csulb.edu
>
> > Is it correct to use the absolute value of the multiplicity in my
> parameters and use the negative values of barrier heights when they are
> exist in the AMBER parameters? Since, I have noticed that in the AMBER
> ff port in GROMACS, the multiplicity values are always set to > 0
> and   the barrier heights have sometime a negative value.
>
>
>
> So my questions are: how to convert it in the gromacs format ?  Is it
> correct to use the absolute value of the multiplicity in my parameters and
> use the negative values of barrier heights when they are exist in the AMBER
> parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the
> multiplicity values are always set to > 0 and   the barrier heights have
> sometime a negative value.
>
>
> Thank you again for your advice.
>
> SA-
>
>
>
>
> Message: 1
>
> Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT)
>
> From: "Austin B. Yongye" 
>
> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
>
> in the  GROMACS format.
>
> To: Discussion list for GROMACS users 
>
> Message-ID:
>
> <1311098935.93905.yahoomailclas...@web161426.mail.bf1.yahoo.com>
>
> Content-Type: text/plain; charset="utf-8"
>
>
>
> It is normal to have combinations of negative and positive values for the
> barrier heights. Those are just the best coefficients to reproduce some QM
> rotational energy curve during the parameterization.  The negative
> periodicities are a convention from AMBER. They simply indicate that the
> dihedral angle potential has more than one term. For your example below:
>
>
>
>
> O2-P
>
>   -OS-CP   10.10  0.0-3. Dimethyl
> phosphate
>
>  1   -0.50  0.0-2.
>
>
>
>   10.10
>
>   0.0 1
>
> -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive
> value is reached, terms for the O2-P-OS-CP potential have been completely
> accounted for.
>
>
>
> Hope that helps.
>
> Austin-
>
>
>
>
>
> --- On Tue, 7/19/11, Mark Abraham  wrote:
>
>
>
> From: Mark Abraham 
>
> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in
> the GROMACS format.
>
> To: "Discussion list for GROMACS users" 
>
> Date: Tuesday, July 19, 2011, 7:08 AM
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On 19/07/2011 11:56 PM, sa wrote:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>   Dear
>
>   GROMCS users,
>
>
>
>   I
>
>   am trying to convert some GLYCAM parameters in GROMACS format.
>
>   For this
>
>   purpose, I am using the latest GLYCAM parameters downloaded
>
>   from the RJ. Woods’
>
>   website and the examples given in the acpype code (here for
>
>   the dihedral angles) :
>
>
>
>
>
>
>
>
>
>
>
>
> http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1
>
>
>
>
>
>
>
>
>
>
>
>
>   ---
>
> # dihedralidivfbarrier hight/2 kcal/mol  phase degrees
> periodicity comments
>
>X -ca-ca-X4   14.500* 180.000
>  2.000 intrpol.bsd.on C6H6
>
>
>
> * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in
> topolbuild, why?) = 30.334 or 15.167 kJ/mol
>
> # X -CA-CA-X4   14.50180.0 2.
> intrpol.bsd.on C6H6 (from parm99.dat)
>
>
>
> # X-CA-CA-X 330.33400 0.0   -30.33400 0.0
> 0.0 0.0   ; intrpol.bsd.on C6H6
>
>
>
> ---
>
>
>
>   I have no problems with the parameters for proteins. But, in case of
> the GLYCAM parameters, I am a little confused
>
>
>
> about the conversion of dihedral force constants (DFC), especially when the
> DFC and the periodicity values are < 0 for example
>
> for this torsion:
>
>
>
>
>
>   O2-P
>
>   -OS-CP   10.10  0.0-3. Dimethyl
> phosphate
>
> 1   -0.50  0.0-2.
>
>
>
>   10.10
>
>   0.0 1
>
>
>
>
>
>
>
> Where only a positive value makes sense, sometimes people use
>
> negative values to indicate some special functional form. Th

Re: [gmx-users] Simulation a labeled protein

[Itamar Kass]

Hi Faezeh,

You can modify the FF and add the Cys-label parameters to the *rtp and 
*hdb files, such that pdb2gmx will be able to use them. Another why is 
use the original pdb as a starting point and modify the output *gto, 
*itp and *top files.


Just remember that in anycase, it is better to copy the files into your 
local directory so an change you made will not effect other simulations.


Cheers,
Itamar


PS I can recommend on this site which can help you in the process 
http://compbio.biosci.uq.edu.au/atb/


On 21/07/11 7:43 PM, Faezeh Nami wrote:

Dear all

I am trying to simulate a protein which a label  (a small organic 
molecule) is covalently attached to a cysteine. Worth to say there is 
no label in the original pdb file of protein and it was attached to 
the Cys. using a software.
Should I insert the label parameters into the conf.gro file or I need 
to modify a force field? If there is someone who has experiences in 
such systems, please have some advice.


Thanks in advance,
Faezeh






--


"In theory, there is no difference between theory and practice. But, in practice, 
there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@monash.edu


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[gmx-users] multiple molecule interaction

[smriti Sebastian]

hi all,
I am new to GROMACS.I would like to know how we will simulate putting more
than two or more molecules of same proteins inside the box and do
simulation?Is there any possibility to replace 100 atoms or so of solvent
with proteins?
Please help.

Regards,
smriti
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Re: [gmx-users] About -chainsep and -ter

[Justin A. Lemkul]

Hsin-Lin Chiang wrote:

於 2011/7/21 上午 03:19, gmx-users-requ...@gromacs.org 提到:

Hi everyone,
>  >  My pdb file is consist of  two chains with one intra- two
>  inter-disulfide bonds.
>  So I used pdb2gmx in this way
>  pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q 
-chainsep ter

>  (I have deleted the TER and OXT lines of A-chain.)
>  I'm not sure if I need to use -ter here, I don't understand the 
meaning

>  of "interective termini selection, iso charged ."
The -ter option allows you to change the protonation state of the 
termini.  The

shorthand "iso" means "instead of," implying that charged termini are the
default.  If you do not need to alter the protonation state of the 
termini, then

you do not need the -ter option.

Thanks for the explain.
>  Anyway, I met problem after editconf, genbox, grompp, genion, and 
grompp.

>  When I execute mdrun,
>  I got the warning and terminated.
>  Please see the long message below my name.
Your system exploded because pdb2gmx likely tried to make your two 
chains one
continuous protein, forming an unrealistic bond between the C-terminal 
of chain

A and the N-terminal of chain B.  By removing the TER delimiter, you've
essentially told pdb2gmx that you have one protein, not two.
If I don't use -chainsep ter, then pdb2gmx will consider two chains as 
Protein-A and Protein-B.

The inter-disulfide bonds between two-chains will be lost.

>  However, if I used pdb2gmx in this way
>  pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep
>  interactive
>  and selected y.
>  Then everything is OK in mdrun step.
>  I don't know what the different in -chainsep interactive and 
-chainsep

>  ter is in my case.
Assuming that the "y" response indicates that you want separate 
chains, that's
why this approach works.  Regardless, if you have two distinct 
proteins (i.e.
the backbones are not continuous), you do not want the chains to be 
considered

continuous.  Disulfides are created in a separate mechanism utilizing
specbond.dat and is independent of the use of -chainsep.

The question is ,
Merge chain ending with residue ASN21 (chain id 'A', atom 163OXT) with 
chain starting with

residue PHE1 (chain id 'B', atom 165 N)? [n/y]

Then I choose y, I think it's the same as -chainsep ter. Isn' it?
But for -chainsep ter, there is errors in mdrun.
For -chainsep interactive and type "y", everything correct.


Please post a diff of the two topologies (the one that failed and the one that 
worked).


-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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Re: [gmx-users] multiple molecule interaction

[Justin A. Lemkul]

smriti Sebastian wrote:

hi all,
I am new to GROMACS.I would like to know how we will simulate putting 
more than two or more molecules of same proteins inside the box and do 
simulation?Is there any possibility to replace 100 atoms or so of 
solvent with proteins?


You can use editconf -center to place any molecule anywhere within a box.  Do 
this as many times as you need and concatenate the resulting coordinate files.


Regarding replacing solvent with protein, that's a bit difficult.  The genbox 
mechanism does the opposite - when provided with the coordinates of a solute, it 
adds solvent into the box and removes solvent molecules when they overlap with 
the solute.  I do not believe there is a targeted way to remove a specific 
number of water molecules and replace them with a protein, but genbox should 
have the same effect.


-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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Re: [gmx-users] multiple molecule interaction

[Mark Abraham]

On 21/07/2011 9:27 PM, smriti Sebastian wrote:

hi all,
I am new to GROMACS.I would like to know how we will simulate putting 
more than two or more molecules of same proteins inside the box and do 
simulation?Is there any possibility to replace 100 atoms or so of 
solvent with proteins?


The same way you do it for a single protein. Get a starting 
configuration that suits you, use pdb2gmx on it, and solvate it with 
genbox. There are other approaches you can use if you have pre-existing 
molecule.itp files.


Mark
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Re: [gmx-users] SPC/E water for Charmm ff implementation

[Mark Abraham]

On 21/07/2011 4:26 PM, E. Nihal Korkmaz wrote:
Thanks but I already checked the literature. What I want to do is, to 
be able to trace down the parameters in the nonbonded file like it can 
be done for any version of gromos. There are slight changes among 
different force fields and I'd like to be able to find that. When I 
find where it reads spc/e parameters for c27, i want to play with the 
parameters that's why i am asking the file read.


Anything that's not found in spce.itp is looked up from ffbonded.itp or 
ffnonbonded.itp. I can't think of a single case where the charges in 
ffnonbonded.itp are used, so there's probably no reason to expect them 
to be correct. You should satisfy yourself that GROMACS is implementing 
the correct form of SPC/E found in the primary literature. However, 
since CHARMM was not parameterized with SPC/E, there probably is no 
particular correct form to use.


Mark



Thanks,
Nihal

On Wed, Jul 20, 2011 at 11:05 PM, Mark Abraham 
mailto:mark.abra...@anu.edu.au>> wrote:


On 21/07/2011 12:59 PM, E. Nihal Korkmaz wrote:

Dear all,

I was trying to see the LJ parameters for SPC/E water in
Charmm27.ff implementation in Gromacs. In the ffnonbonded.itp
file i can see parameters for TIP3P, TIP4P, SPC but not for
SPC/E. Does SPC/E use the same parameters with SPC? (but the
charges listed in the ffnonbonded.itp is different than the
ones listed in spce.itp)


Why not check out the primary literature? Search GROMACS manual
for SPC, follow the reference link for the relevant citation.

Mark
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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 






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Re: [gmx-users] problems about number of frames in the edr file

[Mark Abraham]

On 21/07/2011 3:04 AM, Zhuyi Xue wrote:

Hi, there,

I have a edr file that looks containing about 2000 frames based on its 
size as well as the result from gmxcheck:


frame: 75151040 (index  0), t: 150302.094
Reading energy frame  2 time 150320.000
Timesteps at t=150310 don't match (7.90625, 10)
Reading energy frame   2000 time 170300.016
Timesteps at t=172690 don't match (10, 5.64062)
Last energy frame read 2240 time 172695.656

Found 2241 frames.

But when I use g_energy to get the temperature of each frame in this 
edr file, only 4 frames could be extracted, the last 10 lines of the 
result xvg file is as following:


@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Temperature"
  150302.093750  301.350067
  150310.00  299.902710
  150320.00  303.125641
  150330.00  300.704010

I have tried eneconv to fix it, but no luck. How to could fix it and 
get the values for all frames?


The energy file format contains various quantities related to the 
running average and running squared deviation. These require the time 
step to be the same between each frame. As such, the analysis tools 
expect the time step not to change. Some tools get confused if it does 
change. eneconv -settime allows you to artificially manipulate the 
times, if you think you have a good reason for concatenating the 
energies from dislocated chunks of a trajectory. As soon as you do so, 
the averages and fluctuations reported by g_energy are wrong.


Doing restarts with mdrun -append in the manner suggested on the GROMACS 
webpage will avoid needing to deal with any of this stuff.


Mark

Another question is what does it mean that the timesteps at t=... 
don't match? Will it affect the result of eneconv when connecting 
multiple edr files?


Thank you
Zhuyi


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[gmx-users] g_cluster error in rhombic dodecahedric system

[Anna Marabotti]

Hi folks
here I am with another kind of error, this time analysing my trajectory of
the rhombic dodecahedron dimeric system with g_cluster.
I used the following command:
g_cluster -f prot_boxdodfull_mol.xtc s prot_boxdodfull_molren.tpr -o
prot_boxdodfull_clust.xpm -sz prot_boxdodfull_clustsize.xvg -tr
prot_boxdodfull_clusttrans.xpm -ntr prot_boxdodfull_clusttrans.xvg -clid
prot_boxdodfull_clustovertime.xvg -cl prot_boxdodfull_clusters.pdb -av
-cutoff 0.25 -method gromos -b 1
 
(the command is inspired to that shown in Tsjerk's tutorial, with some
changes, and with the missing -g flag - I forgot to add it). For both least
square fit+RMSD calculation and output I used option 2 (Protein-H).
 
The .tpr file is derived from the renumbered .gro file in which I can see
both subunits of my protein (as suggested sometimes ago by Justin), created
with the command: grompp -f full.mdp -c prot_boxdodfull_molren.gro -o
prot_boxdodfull_molren.tpr -p topol.top, in which full.mdp is the file I
used for the full MD.
 
With this command, I obtained the following output, that I'm copying and
pasting here (I cut some parts because of the length of the message, but I
think they are not necessary):
Reading frame 0 time 1.000 

Reading frame 1 time 10005.000 

Reading frame 2 time 10010.000 

Reading frame 3 time 10015.000 

Reading frame 4 time 10020.000 

Reading frame 5 time 10025.000 

Reading frame 6 time 10030.000 



Reading frame 3000 time 25000.000 

Reading frame 4000 time 3.000 

Last frame 4000 time 3.000 

Allocated 280347120 bytes for frames

Read 4001 frames from trajectory prot_boxdodfull_mol.xtc

Computing 4001x4001 RMS deviation matrix

# RMSD calculations left: 7998000 

# RMSD calculations left: 7994001 

# RMSD calculations left: 7990003 

# RMSD calculations left: 7986006 


...

The RMSD ranges from 0.0776069 to 0.282556 nm
Average RMSD is 0.18743
Number of structures for matrix 4001
Energy of the matrix is 281.481 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0776069
Making list of neighbors within cutoff   

Finding clusters   1

Found 1 clusters

Writing average structure for each cluster to prot_boxdodfull_clusters.pdb
Counted 0 transitions in total, max 0 between two specific clusters

---
Program g_cluster, VERSION 4.5.3
Source code file: matio.c, line: 953

Fatal error:
hi (0.00) <= lo (0.00)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


I tried to look at the documentation, but found only 1 similar problem,
using the g_rmsdist command, but there is not a solution to the problem. I
see the warning message claiming that the rmsd minimum 0 is below lowest
rmsd value, but I don't know how to manage it. Could the .tpr file I used be
the cause of the problem?
Could anybody help me please?
Thank you so much for your continue support
Anna
 
__
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"
(Roberto Benigni, about Roberto Saviano)
 
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Re: [gmx-users] g_cluster error in rhombic dodecahedric system

[Mark Abraham]

On 21/07/2011 11:38 PM, Anna Marabotti wrote:

Hi folks
here I am with another kind of error, this time analysing my 
trajectory of the rhombic dodecahedron dimeric system with g_cluster.

I used the following command:
g_cluster -f prot_boxdodfull_mol.xtc s prot_boxdodfull_molren.tpr -o 
prot_boxdodfull_clust.xpm -sz prot_boxdodfull_clustsize.xvg -tr 
prot_boxdodfull_clusttrans.xpm -ntr prot_boxdodfull_clusttrans.xvg 
-clid prot_boxdodfull_clustovertime.xvg -cl 
prot_boxdodfull_clusters.pdb -av -cutoff 0.25 -method gromos -b 1


I'd suggest starting with a small trajectory and a basic clustering 
method to help you eliminate possible sources of problems. If things are 
working, add complexity.


(the command is inspired to that shown in Tsjerk's tutorial, with some 
changes, and with the missing -g flag - I forgot to add it). For both 
least square fit+RMSD calculation and output I used option 2 (Protein-H).
The .tpr file is derived from the renumbered .gro file in which I can 
see both subunits of my protein (as suggested sometimes ago by 
Justin), created with the command: grompp -f full.mdp -c 
prot_boxdodfull_molren.gro -o prot_boxdodfull_molren.tpr -p topol.top, 
in which full.mdp is the file I used for the full MD.


I don't think you need a new .tpr, or a .tpr at all. Nothing about the 
clustering method requires knowledge of molecule or parameter 
definitions, so the original .tpr or the coordinate file that made it 
will do. Surely the clustering is based on RMS after fitting of the two 
structures under consideration, and now even the coordinates in the 
g_cluster -s file don't matter. Pre-processing the trajectory can matter 
- you probably want whole molecules in the simulation cell.


Mark

With this command, I obtained the following output, that I'm copying 
and pasting here (I cut some parts because of the length of the 
message, but I think they are not necessary):


Reading frame 0 time 1.000

Reading frame 1 time 10005.000

Reading frame 2 time 10010.000

Reading frame 3 time 10015.000

Reading frame 4 time 10020.000

Reading frame 5 time 10025.000

Reading frame 6 time 10030.000



Reading frame 3000 time 25000.000

Reading frame 4000 time 3.000

Last frame 4000 time 3.000

Allocated 280347120 bytes for frames

Read 4001 frames from trajectory prot_boxdodfull_mol.xtc

Computing 4001x4001 RMS deviation matrix

# RMSD calculations left: 7998000

# RMSD calculations left: 7994001

# RMSD calculations left: 7990003

# RMSD calculations left: 7986006

...

The RMSD ranges from 0.0776069 to 0.282556 nm
Average RMSD is 0.18743
Number of structures for matrix 4001
Energy of the matrix is 281.481 nm
WARNING: rmsd minimum 0 is below lowest rmsd value 0.0776069
Making list of neighbors within cutoff

Finding clusters1

Found 1 clusters

Writing average structure for each cluster to prot_boxdodfull_clusters.pdb
Counted 0 transitions in total, max 0 between two specific clusters

---
Program g_cluster, VERSION 4.5.3
Source code file: matio.c, line: 953

Fatal error:
hi (0.00) <= lo (0.00)
For more information and tips for troubleshooting, please check the 
GROMACS

website at http://www.gromacs.org/Documentation/Errors
---

I tried to look at the documentation, but found only 1 similar 
problem, using the g_rmsdist command, but there is not a solution to 
the problem. I see the warning message claiming that the rmsd minimum 
0 is below lowest rmsd value, but I don't know how to manage it. Could 
the .tpr file I used be the cause of the problem?

Could anybody help me please?
Thank you so much for your continue support
Anna
__
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
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E-mail: amarabo...@isa.cnr.it 
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[gmx-users] Parameters for DMPG and G53a6 force field

[Krzysztof Mlynarczyk]

Hello,
I need parameters for DMPG membrane (G53a6 force field). Does anybody know
where I could find a tested parameter set and pdb file? If not, I believe I
could construct my own from e.g. Kukol A, Lipid Models for United-Atom
Molecular Dynamics Simulations of Proteins, DOI: 10.1021/ct8003468 by
merging PG parameters from POPG and the rest of the molecule from DMPC.

Thank you,
Christopher
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[gmx-users] About -chainsep and -ter

[Hsin-Lin Chiang]

> Please post a diff of the two topologies (the one that failed and the one 
> that 
> worked). 
> 
> -Justin 
I use diff bash commend on the two top file and save to log file.
The different was long but they both have three inter-disulfide bond
There are 3973 lines in different log file.  
I'm not sure if I can post all here.
Do we have another way to discuss?

Sincerely yours,
Hsin-Lin
 
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Re: [gmx-users] About -chainsep and -ter

[Justin A. Lemkul]

Hsin-Lin Chiang wrote:
**> Please post a diff of the two topologies (the one that failed and 
the one that

 > worked).
 >
 > -Justin
I use diff bash commend on the two top file and save to log file.
The different was long but they both have three inter-disulfide bond
There are 3973 lines in different log file. 
I'm not sure if I can post all here.

Do we have another way to discuss?



If you send me your two topologies (off-list), I will take a look at them to see 
if I can figure out what happened.


-Justin

--


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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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[gmx-users] Velocity generation

[Juliette N.]

Dear gmx users,

I have two short questions about generation of initial velocities in
simulations. If I want to run simulations at for example 400 K do I have to
alter the temperature for maxwell distribution settings? ( I mean
gen_temp=  400? )

gen_vel =  yes
gen_temp=  300.0 > 400 ?
gen_seed=  173529

- Also If I want to do simulated annealing for the target T= 400 K, should I
anneal to higher T than 400, say 500K and cool down to 400 or SA is only
applicable at lower target temperatures like 300K ?


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J.
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Re: [gmx-users] Velocity generation

[Justin A. Lemkul]

Juliette N. wrote:

Dear gmx users,
 
I have two short questions about generation of initial velocities in 
simulations. If I want to run simulations at for example 400 K do I have 
to alter the temperature for maxwell distribution settings? ( I mean 
gen_temp=  400? )



Yes, otherwise the initial velocity distribution is wrong and your thermostat 
will have to make some large compensations to reach the target temperature.


gen_vel =  yes 
gen_temp=  300.0 > 400 ?  
gen_seed=  173529   

- Also If I want to do simulated annealing for the target T= 400 K, 
should I anneal to higher T than 400, say 500K and cool down to 400 or 
SA is only applicable at lower target temperatures like 300K ?
 


You can do whatever you like.  People sometimes even use SA up to 1000 K or 
more.

-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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[gmx-users] R: Re: g_cluster error in rhombic dodecahedric system (Mark Abraham)

[Anna Marabotti]

Thanks Mark for suggestion, I'll try to do a simpler clustering method. In
the meantime, I only would like to add a further info: I pre-processed my
trajectory following someone's (Justin, IIRC) suggestion in a previous
message, using trjconv -pbc mol -ur compact. So, in my trajectory the
molecules should be whole (at least, I see my protein as a whole). This
pre-processing was necessary because with trjconv -pbc whole I was not able
to have my homodimeric protein in the unit cell: the protein was split in
two monomers in two adjacent unit cells. Could be the presence of the two
identical monomers to "confuse" Gromacs that sees an RMSD minimum of 0?
Anna

-Messaggio originale-

Message: 2
Date: Fri, 22 Jul 2011 00:25:03 +1000
From: Mark Abraham 
Subject: Re: [gmx-users] g_cluster error in rhombic dodecahedric
system
To: Discussion list for GROMACS users 
Message-ID: <4e2836bf.3000...@anu.edu.au>
Content-Type: text/plain; charset="iso-8859-1"

On 21/07/2011 11:38 PM, Anna Marabotti wrote:
> Hi folks
> here I am with another kind of error, this time analysing my 
> trajectory of the rhombic dodecahedron dimeric system with g_cluster.
> I used the following command:
> g_cluster -f prot_boxdodfull_mol.xtc s prot_boxdodfull_molren.tpr -o 
> prot_boxdodfull_clust.xpm -sz prot_boxdodfull_clustsize.xvg -tr 
> prot_boxdodfull_clusttrans.xpm -ntr prot_boxdodfull_clusttrans.xvg 
> -clid prot_boxdodfull_clustovertime.xvg -cl 
> prot_boxdodfull_clusters.pdb -av -cutoff 0.25 -method gromos -b 1

I'd suggest starting with a small trajectory and a basic clustering 
method to help you eliminate possible sources of problems. If things are 
working, add complexity.

> (the command is inspired to that shown in Tsjerk's tutorial, with some 
> changes, and with the missing -g flag - I forgot to add it). For both 
> least square fit+RMSD calculation and output I used option 2 (Protein-H).
> The .tpr file is derived from the renumbered .gro file in which I can 
> see both subunits of my protein (as suggested sometimes ago by 
> Justin), created with the command: grompp -f full.mdp -c 
> prot_boxdodfull_molren.gro -o prot_boxdodfull_molren.tpr -p topol.top, 
> in which full.mdp is the file I used for the full MD.

I don't think you need a new .tpr, or a .tpr at all. Nothing about the 
clustering method requires knowledge of molecule or parameter 
definitions, so the original .tpr or the coordinate file that made it 
will do. Surely the clustering is based on RMS after fitting of the two 
structures under consideration, and now even the coordinates in the 
g_cluster -s file don't matter. Pre-processing the trajectory can matter 
- you probably want whole molecules in the simulation cell.

Mark

> With this command, I obtained the following output, that I'm copying 
> and pasting here (I cut some parts because of the length of the 
> message, but I think they are not necessary):
>
> Reading frame 0 time 1.000
>
> Reading frame 1 time 10005.000
>
> Reading frame 2 time 10010.000
>
> Reading frame 3 time 10015.000
>
> Reading frame 4 time 10020.000
>
> Reading frame 5 time 10025.000
>
> Reading frame 6 time 10030.000
>
> 
>
> Reading frame 3000 time 25000.000
>
> Reading frame 4000 time 3.000
>
> Last frame 4000 time 3.000
>
> Allocated 280347120 bytes for frames
>
> Read 4001 frames from trajectory prot_boxdodfull_mol.xtc
>
> Computing 4001x4001 RMS deviation matrix
>
> # RMSD calculations left: 7998000
>
> # RMSD calculations left: 7994001
>
> # RMSD calculations left: 7990003
>
> # RMSD calculations left: 7986006
>
>

...
>
> The RMSD ranges from 0.0776069 to 0.282556 nm
> Average RMSD is 0.18743
> Number of structures for matrix 4001
> Energy of the matrix is 281.481 nm
> WARNING: rmsd minimum 0 is below lowest rmsd value 0.0776069
> Making list of neighbors within cutoff
>
> Finding clusters1
>
> Found 1 clusters
>
> Writing average structure for each cluster to prot_boxdodfull_clusters.pdb
> Counted 0 transitions in total, max 0 between two specific clusters
>
> ---
> Program g_cluster, VERSION 4.5.3
> Source code file: matio.c, line: 953
>
> Fatal error:
> hi (0.00) <= lo (0.00)
> For more information and tips for troubleshooting, please check the 
> GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> I tried to look at the documentation, but found only 1 similar 
> problem, using the g_rmsdist command, but there is not a solution to 
> the problem. I see the warning message claiming that the rmsd minimum 
> 0 is below lowest rmsd value, but I don't know how to manage it. Could 
> the .tpr file I used be the cause of the problem?
> Could anybody help me please?
> Thank you so much for your continue support
> Anna
> ___

Re: [gmx-users] About -chainsep and -ter

[Justin A. Lemkul]

I suspect this is a bug, so I have filed an issue on redmine:

http://redmine.gromacs.org/issues/784

In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep 
interactive" option did not work, but now it does.  Conversely, "-chainsep ter" 
(which should also work in this case) does not.


-Justin

Hsin-Lin Chiang wrote:
**> Please post a diff of the two topologies (the one that failed and 
the one that

 > worked).
 >
 > -Justin
I use diff bash commend on the two top file and save to log file.
The different was long but they both have three inter-disulfide bond
There are 3973 lines in different log file. 
I'm not sure if I can post all here.

Do we have another way to discuss?

Sincerely yours,
Hsin-Lin



--


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: Re: g_cluster error in rhombic dodecahedric system (Mark Abraham)

[Tsjerk Wassenaar]

Hi Anna,

On Thu, Jul 21, 2011 at 5:11 PM, Anna Marabotti
 wrote:
> Thanks Mark for suggestion, I'll try to do a simpler clustering method. In
> the meantime, I only would like to add a further info: I pre-processed my
> trajectory following someone's (Justin, IIRC) suggestion in a previous
> message, using trjconv -pbc mol -ur compact. So, in my trajectory the
> molecules should be whole (at least, I see my protein as a whole). This
> pre-processing was necessary because with trjconv -pbc whole I was not able
> to have my homodimeric protein in the unit cell: the protein was split in
> two monomers in two adjacent unit cells. Could be the presence of the two
> identical monomers to "confuse" Gromacs that sees an RMSD minimum of 0?
> Anna

No, the output says the RMSD ranges from 0.07 to 0.28. The problem
arises because you only get one cluster using a cutoff of 0.25 nm. If
you're certain there are some clusters to be identified, despite the
low RMSD values that sort of indicate there is not much variation,
then you can lower the cutoff. The error also does not pertain to the
RMSD matrix, but probably to the matrix of transitions, because there
aren't any. Please do note that this has absolutely nothing to do with
using a rhombic dodecahedron :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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[gmx-users] large error bars in PMF

[Rebeca García Fandiño]

Hi,
I am trying to calculate the binding energy of two molecules using the PMF 
(Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have written to the list because changing the number of 
windows used in the Umbrella Sampling calculations different results were 
obtained, and I was suggested to extend my simulations since the error bars 
associated to each windows were too high.
I have now extended my simulations from 1 ns to 8 ns, however, I cannot see 
much different from the shorter calculations. I send you the comparison of the 
two PMF including the error bars (attached).
Now I am using 50 windows, but the shorter simulations were done using 100 
windows, so I don't think increasing the number of windows could help. 
My system has about 29200 atoms (where 29000 are chloroform atoms). The *mdp 
file I am using is copied below. 
Would you have any suggestion to improve the results and decrease the error 
bars in the calculations?

MDP file---
title   = Umbrella pulling simulation
define  =
define  =
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 50   ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 5000
nstxtcout   = 5000  ; every 10 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = ACH   CL3
tau_t   = 0.5   0.5
ref_t   = 300   300
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = r_1
pull_group1 = r_2
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps

---


Thanks a lot in advance.

Best wishes,

Dr. Rebeca Garcia
Santiago de Compostela University
Spain



  

comparation_shorter_longer_PMF.pdf
Description: Adobe PDF document
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[gmx-users] About -chainsep and -ter

[Hsin-Lin Chiang]

>I suspect this is a bug, so I have filed an issue on redmine:
>
>http://redmine.gromacs.org/issues/784
>
>In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep 
>interactive" option did not work, but now it does. Conversely, "-chainsep ter" 
>(which should also work in this case) does not.
>
>-Justin

I get success in pdb2gmx, but I not only delete ter line but also all OXT lines 
according to this mailing list,

http://www.mail-archive.com/gmx-users@gromacs.org/msg33251.html

But I'm failed when I used mdrun in "-chainsep ter" case.

Hsin-Lin

 
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Re: [gmx-users] About -chainsep and -ter

[Justin A. Lemkul]

Hsin-Lin Chiang wrote:

I suspect this is a bug, so I have filed an issue on redmine:

http://redmine.gromacs.org/issues/784

In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep 
interactive" option did not work, but now it does.  Conversely, "-chainsep ter" 
(which should also work in this case) does not.


-Justin




I get success in pdb2gmx, but I not only delete ter line but also all OXT lines 
according to this mailing list,

http://www.mail-archive.com/gmx-users@gromacs.org/msg33251.html

But I'm failed when I used mdrun in "-chainsep ter" case.




Right.  Even if you somehow force pdb2gmx to write a topology in this case, the 
bonds are not correct and the termini are incomplete.  That will hopefully be 
resolved when the bug is fixed.  For now, you have a workaround.  Just use 
"-chainsep interactive" and you will get a proper topology.


-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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Re: [gmx-users] large error bars in PMF

[Justin A. Lemkul]

Rebeca García Fandiño wrote:


Hi,
I am trying to calculate the binding energy of two molecules using the 
PMF (Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have written to the list because changing the number of 
windows used in the Umbrella Sampling calculations different results 
were obtained, and I was suggested to extend my simulations since the 
error bars associated to each windows were too high.
I have now extended my simulations from 1 ns to 8 ns, however, I cannot 
see much different from the shorter calculations. I send you the 
comparison of the two PMF including the error bars (attached).
Now I am using 50 windows, but the shorter simulations were done using 
100 windows, so I don't think increasing the number of windows could help.
My system has about 29200 atoms (where 29000 are chloroform atoms). The 
*mdp file I am using is copied below.
Would you have any suggestion to improve the results and decrease the 
error bars in the calculations?




Neither of the PMF profiles look converged.  In the case of 8-ns sampling, you 
do not have a well-defined energy minimum and the whole plot is very rough. 
This suggests to me that you still need more sampling time.  Keep in mind that 
even 8 ns is a very tiny amount of sampling in each window.


What is it that you're trying to pull?  What are r_1 and r_2?  Are they 
components of a small peptide or something else?  It looks as if the total DG is 
going to be somewhere on the order of 6 kcal/mol, so if you want reasonable 
error bars you will not lots of well-converged data.


-Justin


MDP file---
title   = Umbrella pulling simulation
define  =
define  =
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 50   ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 5000
nstxtcout   = 5000  ; every 10 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = ACH   CL3
tau_t   = 0.5   0.5
ref_t   = 300   300
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = r_1
pull_group1 = r_2
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps

---


Thanks a lot in advance.

Best wishes,

Dr. Rebeca Garcia
Santiago de Compostela University
Spain




--


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] large error bars in PMF

[Rebeca García Fandiño]

Hi,
thanks a lot for your quick answer.
What I am trying to pull are two small peptides one from another (r_1 and r_2). 
I did not understand very well your last suggestion: "...if you want reasonable 
error bars you will not lots of well-converged data". 
Do you mean I will need also more windows besides extending the simulations?
I think the problem could be also that the peptides I am using rotate in the 
box and they do not remain flat one respect to the other. They gyrate freely 
and some parts of their structure interact along the pulling...
Thanks a lot again for your help.
Best wishes,
Rebeca.



From: rega...@hotmail.com
To: gmx-users@gromacs.org
Date: Thu, 21 Jul 2011 16:36:59 +
Subject: [gmx-users] large error bars in PMF













Hi,
I am trying to calculate the binding energy of two molecules using the PMF 
(Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have written to the list because changing the number of 
windows used in the Umbrella Sampling calculations different results were 
obtained, and I was suggested to extend my simulations since the error bars 
associated to each windows were too high.
I have now extended my simulations from 1 ns to 8 ns, however, I cannot see 
much different from the shorter calculations. I send you the comparison of the 
two PMF including the error bars (attached).
Now I am using 50 windows, but the shorter simulations were done using 100 
windows, so I don't think increasing the number of windows could help. 
My system has about 29200 atoms (where 29000 are chloroform atoms). The *mdp 
file I am using is copied below. 
Would you have any suggestion to improve the results and decrease the error 
bars in the calculations?

MDP file---
title   = Umbrella pulling simulation
define  =
define  =
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 50   ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 5000
nstxtcout   = 5000  ; every 10 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = ACH   CL3
tau_t   = 0.5   0.5
ref_t   = 300   300
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = r_1
pull_group1 = r_2
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps

---


Thanks a lot in advance.

Best wishes,

Dr. Rebeca Garcia
Santiago de Compostela University
Spain



  

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Re: [gmx-users] large error bars in PMF

[Justin A. Lemkul]

Rebeca García Fandiño wrote:

Hi,
thanks a lot for your quick answer.
What I am trying to pull are two small peptides one from another (r_1 
and r_2).
I did not understand very well your last suggestion: "...if you want 
reasonable error bars you will not lots of well-converged data".


Oops, that should have read "you will *need* lots of well-converged data."


Do you mean I will need also more windows besides extending the simulations?


I doubt you need more windows.  Likely you just need more time in each.

I think the problem could be also that the peptides I am using rotate in 
the box and they do not remain flat one respect to the other. They 
gyrate freely and some parts of their structure interact along the 
pulling...


Interactions are part of the dissociation process and are not problematic per 
se.  But if you're trying to obtain only a one-dimensional PMF then your 
rotation could be a problem.  Is there some reason you need a one-dimensional 
PMF and not a three-dimensional PMF?  What are you trying to achieve?


-Justin


Thanks a lot again for your help.
Best wishes,
Rebeca.




From: rega...@hotmail.com
To: gmx-users@gromacs.org
Date: Thu, 21 Jul 2011 16:36:59 +
Subject: [gmx-users] large error bars in PMF


Hi,
I am trying to calculate the binding energy of two molecules using the 
PMF (Umbrella Sampling method) and Gromacs 4.0.
Some weeks ago I have written to the list because changing the number of 
windows used in the Umbrella Sampling calculations different results 
were obtained, and I was suggested to extend my simulations since the 
error bars associated to each windows were too high.
I have now extended my simulations from 1 ns to 8 ns, however, I cannot 
see much different from the shorter calculations. I send you the 
comparison of the two PMF including the error bars (attached).
Now I am using 50 windows, but the shorter simulations were done using 
100 windows, so I don't think increasing the number of windows could help.
My system has about 29200 atoms (where 29000 are chloroform atoms). The 
*mdp file I am using is copied below.
Would you have any suggestion to improve the results and decrease the 
error bars in the calculations?


MDP file---
title   = Umbrella pulling simulation
define  =
define  =
; Run parameters
integrator  = md
dt  = 0.002
tinit   = 0
nsteps  = 50   ; 1 ns
nstcomm = 10
; Output parameters
nstxout = 5000 ; every 10 ps
nstvout = 5000
nstfout = 5000
nstxtcout   = 5000  ; every 10 ps
nstenergy   = 5000
; Bond parameters
constraint_algorithm= lincs
constraints = all-bonds
continuation= yes
; Single-range cutoff scheme
nstlist = 5
ns_type = grid
rlist   = 1.4
rcoulomb= 1.4
rvdw= 1.4
; PME electrostatics parameters
coulombtype = PME
fourierspacing  = 0.12
fourier_nx  = 0
fourier_ny  = 0
fourier_nz  = 0
pme_order   = 4
ewald_rtol  = 1e-5
optimize_fft= yes
; Berendsen temperature coupling is on in two groups
Tcoupl  = Nose-Hoover
tc_grps = ACH   CL3
tau_t   = 0.5   0.5
ref_t   = 300   300
; Pressure coupling is on
Pcoupl  = Parrinello-Rahman
pcoupltype  = isotropic
tau_p   = 1.0
compressibility = 4.5e-5
ref_p   = 1.0
; Generate velocities is off
gen_vel = no
; Periodic boundary conditions are on in all directions
pbc = xyz
; Long-range dispersion correction
DispCorr= EnerPres
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = r_1
pull_group1 = r_2
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps

---


Thanks a lot in advance.

Best wishes,

Dr. Rebeca Garcia
Santiago de Compostela University
Spain



-- gmx-users mailing list gmx-users@gromacs.org 
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archive at http://www.gromacs.org/Support/Mailing_Lists/Search before 
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Read http://www.gromacs.org/Support/Mailing_Lists




--


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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Please search the archive at 
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Re: [gmx-users] large error bars in PMF

[Justin A. Lemkul]

Justin A. Lemkul wrote:



Rebeca García Fandiño wrote:

Hi,
thanks a lot for your quick answer.
What I am trying to pull are two small peptides one from another (r_1 
and r_2).
I did not understand very well your last suggestion: "...if you want 
reasonable error bars you will not lots of well-converged data".


Oops, that should have read "you will *need* lots of well-converged data."

Do you mean I will need also more windows besides extending the 
simulations?


I doubt you need more windows.  Likely you just need more time in each.

I think the problem could be also that the peptides I am using rotate 
in the box and they do not remain flat one respect to the other. They 
gyrate freely and some parts of their structure interact along the 
pulling...


Interactions are part of the dissociation process and are not 
problematic per se.  But if you're trying to obtain only a 
one-dimensional PMF then your rotation could be a problem.  Is there 
some reason you need a one-dimensional PMF and not a three-dimensional 
PMF?  What are you trying to achieve?




I should also add that if you're getting spurious interactions across periodic 
boundaries, this is a problem.  In that case, you need a different type of box, 
like a dodecahedron for spherical symmetry.


-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


--
gmx-users mailing listgmx-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!
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

FW: [gmx-users] large error bars in PMF

[Rebeca García Fandiño]

I am trying to achieve the binding energy of the dimer composed by the two 
small cyclic peptides, to compare it with experimental. What advantages would I 
have using 3D PMF instead only 1D for this calculation?
Thanks a lot!
Rebeca.

> Date: Thu, 21 Jul 2011 14:14:44 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] large error bars in PMF
> 
> 
> 
> Rebeca García Fandiño wrote:
> > Hi,
> > thanks a lot for your quick answer.
> > What I am trying to pull are two small peptides one from another (r_1 
> > and r_2).
> > I did not understand very well your last suggestion: "...if you want 
> > reasonable error bars you will not lots of well-converged data".
> 
> Oops, that should have read "you will *need* lots of well-converged data."
> 
> > Do you mean I will need also more windows besides extending the simulations?
> 
> I doubt you need more windows.  Likely you just need more time in each.
> 
> > I think the problem could be also that the peptides I am using rotate in 
> > the box and they do not remain flat one respect to the other. They 
> > gyrate freely and some parts of their structure interact along the 
> > pulling...
> 
> Interactions are part of the dissociation process and are not problematic per 
> se.  But if you're trying to obtain only a one-dimensional PMF then your 
> rotation could be a problem.  Is there some reason you need a one-dimensional 
> PMF and not a three-dimensional PMF?  What are you trying to achieve?
> 
> -Justin
> 
> > Thanks a lot again for your help.
> > Best wishes,
> > Rebeca.
> > 
> > 
> > 
> > 
> > From: rega...@hotmail.com
> > To: gmx-users@gromacs.org
> > Date: Thu, 21 Jul 2011 16:36:59 +
> > Subject: [gmx-users] large error bars in PMF
> > 
> > 
> > Hi,
> > I am trying to calculate the binding energy of two molecules using the 
> > PMF (Umbrella Sampling method) and Gromacs 4.0.
> > Some weeks ago I have written to the list because changing the number of 
> > windows used in the Umbrella Sampling calculations different results 
> > were obtained, and I was suggested to extend my simulations since the 
> > error bars associated to each windows were too high.
> > I have now extended my simulations from 1 ns to 8 ns, however, I cannot 
> > see much different from the shorter calculations. I send you the 
> > comparison of the two PMF including the error bars (attached).
> > Now I am using 50 windows, but the shorter simulations were done using 
> > 100 windows, so I don't think increasing the number of windows could help.
> > My system has about 29200 atoms (where 29000 are chloroform atoms). The 
> > *mdp file I am using is copied below.
> > Would you have any suggestion to improve the results and decrease the 
> > error bars in the calculations?
> > 
> > MDP file---
> > title   = Umbrella pulling simulation
> > define  =
> > define  =
> > ; Run parameters
> > integrator  = md
> > dt  = 0.002
> > tinit   = 0
> > nsteps  = 50   ; 1 ns
> > nstcomm = 10
> > ; Output parameters
> > nstxout = 5000 ; every 10 ps
> > nstvout = 5000
> > nstfout = 5000
> > nstxtcout   = 5000  ; every 10 ps
> > nstenergy   = 5000
> > ; Bond parameters
> > constraint_algorithm= lincs
> > constraints = all-bonds
> > continuation= yes
> > ; Single-range cutoff scheme
> > nstlist = 5
> > ns_type = grid
> > rlist   = 1.4
> > rcoulomb= 1.4
> > rvdw= 1.4
> > ; PME electrostatics parameters
> > coulombtype = PME
> > fourierspacing  = 0.12
> > fourier_nx  = 0
> > fourier_ny  = 0
> > fourier_nz  = 0
> > pme_order   = 4
> > ewald_rtol  = 1e-5
> > optimize_fft= yes
> > ; Berendsen temperature coupling is on in two groups
> > Tcoupl  = Nose-Hoover
> > tc_grps = ACH   CL3
> > tau_t   = 0.5   0.5
> > ref_t   = 300   300
> > ; Pressure coupling is on
> > Pcoupl  = Parrinello-Rahman
> > pcoupltype  = isotropic
> > tau_p   = 1.0
> > compressibility = 4.5e-5
> > ref_p   = 1.0
> > ; Generate velocities is off
> > gen_vel = no
> > ; Periodic boundary conditions are on in all directions
> > pbc = xyz
> > ; Long-range dispersion correction
> > DispCorr= EnerPres
> > ; Pull code
> > pull= umbrella
> > pull_geometry   = distance
> > pull_dim= N N Y
> > pull_start  = yes
> > pull_ngroups= 1
> > pull_group0 = r_1
> > pull_group1 = r_2
> > pull_init1  = 0
> > pull_rate1  = 0.0
> > pull_k1 = 1000  ; kJ mol^-1 nm^-2
> > pull_nstxout= 1000  ; every 2 ps
> > pull_nstfout= 1000  ; every 2 ps
> > 
> > ---
> > 
> > 
> > Thanks a lot in advance.
> > 
> > Best wishes,
> > 
> > Dr. Rebeca Garcia
> > Santiago de Compostela University
> > Spain
> > 
> > 

Re: FW: [gmx-users] large error bars in PMF

[Justin A. Lemkul]

Rebeca García Fandiño wrote:



I am trying to achieve the binding energy of the dimer composed by the 
two small cyclic peptides, to compare it with experimental. What 
advantages would I have using 3D PMF instead only 1D for this calculation?


Intuitively, two molecules diffuse through solution until they find one another, 
which to me sounds a lot like a 3D path.  Further, using a dodecahedral box for 
your umbrella sampling removes the problems you're having with the peptides 
rotating.  It sounds like you're trying to pull in one direction along a 
rectangular box, but the peptides are not playing nice.  I feel like this 
discussion has come up at least once or twice before, though...


-Justin


Thanks a lot!
Rebeca.

 > Date: Thu, 21 Jul 2011 14:14:44 -0400
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] large error bars in PMF
 >
 >
 >
 > Rebeca García Fandiño wrote:
 > > Hi,
 > > thanks a lot for your quick answer.
 > > What I am trying to pull are two small peptides one from another (r_1
 > > and r_2).
 > > I did not understand very well your last suggestion: "...if you want
 > > reasonable error bars you will not lots of well-converged data".
 >
 > Oops, that should have read "you will *need* lots of well-converged 
data."

 >
 > > Do you mean I will need also more windows besides extending the 
simulations?

 >
 > I doubt you need more windows. Likely you just need more time in each.
 >
 > > I think the problem could be also that the peptides I am using 
rotate in

 > > the box and they do not remain flat one respect to the other. They
 > > gyrate freely and some parts of their structure interact along the
 > > pulling...
 >
 > Interactions are part of the dissociation process and are not 
problematic per

 > se. But if you're trying to obtain only a one-dimensional PMF then your
 > rotation could be a problem. Is there some reason you need a 
one-dimensional

 > PMF and not a three-dimensional PMF? What are you trying to achieve?
 >
 > -Justin
 >
 > > Thanks a lot again for your help.
 > > Best wishes,
 > > Rebeca.
 > >
 > >
 > >
 > > 


 > > From: rega...@hotmail.com
 > > To: gmx-users@gromacs.org
 > > Date: Thu, 21 Jul 2011 16:36:59 +
 > > Subject: [gmx-users] large error bars in PMF
 > >
 > >
 > > Hi,
 > > I am trying to calculate the binding energy of two molecules using the
 > > PMF (Umbrella Sampling method) and Gromacs 4.0.
 > > Some weeks ago I have written to the list because changing the 
number of

 > > windows used in the Umbrella Sampling calculations different results
 > > were obtained, and I was suggested to extend my simulations since the
 > > error bars associated to each windows were too high.
 > > I have now extended my simulations from 1 ns to 8 ns, however, I 
cannot

 > > see much different from the shorter calculations. I send you the
 > > comparison of the two PMF including the error bars (attached).
 > > Now I am using 50 windows, but the shorter simulations were done using
 > > 100 windows, so I don't think increasing the number of windows 
could help.
 > > My system has about 29200 atoms (where 29000 are chloroform atoms). 
The

 > > *mdp file I am using is copied below.
 > > Would you have any suggestion to improve the results and decrease the
 > > error bars in the calculations?
 > >
 > > MDP file---
 > > title = Umbrella pulling simulation
 > > define =
 > > define =
 > > ; Run parameters
 > > integrator = md
 > > dt = 0.002
 > > tinit = 0
 > > nsteps = 50 ; 1 ns
 > > nstcomm = 10
 > > ; Output parameters
 > > nstxout = 5000 ; every 10 ps
 > > nstvout = 5000
 > > nstfout = 5000
 > > nstxtcout = 5000 ; every 10 ps
 > > nstenergy = 5000
 > > ; Bond parameters
 > > constraint_algorithm = lincs
 > > constraints = all-bonds
 > > continuation = yes
 > > ; Single-range cutoff scheme
 > > nstlist = 5
 > > ns_type = grid
 > > rlist = 1.4
 > > rcoulomb = 1.4
 > > rvdw = 1.4
 > > ; PME electrostatics parameters
 > > coulombtype = PME
 > > fourierspacing = 0.12
 > > fourier_nx = 0
 > > fourier_ny = 0
 > > fourier_nz = 0
 > > pme_order = 4
 > > ewald_rtol = 1e-5
 > > optimize_fft = yes
 > > ; Berendsen temperature coupling is on in two groups
 > > Tcoupl = Nose-Hoover
 > > tc_grps = ACH CL3
 > > tau_t = 0.5 0.5
 > > ref_t = 300 300
 > > ; Pressure coupling is on
 > > Pcoupl = Parrinello-Rahman
 > > pcoupltype = isotropic
 > > tau_p = 1.0
 > > compressibility = 4.5e-5
 > > ref_p = 1.0
 > > ; Generate velocities is off
 > > gen_vel = no
 > > ; Periodic boundary conditions are on in all directions
 > > pbc = xyz
 > > ; Long-range dispersion correction
 > > DispCorr = EnerPres
 > > ; Pull code
 > > pull = umbrella
 > > pull_geometry = distance
 > > pull_dim = N N Y
 > > pull_start = yes
 > > pull_ngroups = 1
 > > pull_group0 = r_1
 > > pull_group1 = r_2
 > > pull_init1 = 0
 > > pull_rate1 = 0.0
 > > pull_k1 = 100

RE: [gmx-users] large error bars in PMF

[Rebeca García Fandiño]

OK,
I will try a dodecahedral box and also to extend my actual simulations.
Could you give me some advice about starting to learn about 3D PMF? I have not 
seen this in the manual, and I have never used it before. I have only found 
your tutorial about how to calculate PMF in Gromacs 4...
Thanks a lot again for your help.
Best wishes,
Rebeca.

> Date: Thu, 21 Jul 2011 15:16:52 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: FW: [gmx-users] large error bars in PMF
> 
> 
> 
> Rebeca García Fandiño wrote:
> > 
> > 
> > I am trying to achieve the binding energy of the dimer composed by the 
> > two small cyclic peptides, to compare it with experimental. What 
> > advantages would I have using 3D PMF instead only 1D for this calculation?
> 
> Intuitively, two molecules diffuse through solution until they find one 
> another, 
> which to me sounds a lot like a 3D path.  Further, using a dodecahedral box 
> for 
> your umbrella sampling removes the problems you're having with the peptides 
> rotating.  It sounds like you're trying to pull in one direction along a 
> rectangular box, but the peptides are not playing nice.  I feel like this 
> discussion has come up at least once or twice before, though...
> 
> -Justin
> 
> > Thanks a lot!
> > Rebeca.
> > 
> >  > Date: Thu, 21 Jul 2011 14:14:44 -0400
> >  > From: jalem...@vt.edu
> >  > To: gmx-users@gromacs.org
> >  > Subject: Re: [gmx-users] large error bars in PMF
> >  >
> >  >
> >  >
> >  > Rebeca García Fandiño wrote:
> >  > > Hi,
> >  > > thanks a lot for your quick answer.
> >  > > What I am trying to pull are two small peptides one from another (r_1
> >  > > and r_2).
> >  > > I did not understand very well your last suggestion: "...if you want
> >  > > reasonable error bars you will not lots of well-converged data".
> >  >
> >  > Oops, that should have read "you will *need* lots of well-converged 
> > data."
> >  >
> >  > > Do you mean I will need also more windows besides extending the 
> > simulations?
> >  >
> >  > I doubt you need more windows. Likely you just need more time in each.
> >  >
> >  > > I think the problem could be also that the peptides I am using 
> > rotate in
> >  > > the box and they do not remain flat one respect to the other. They
> >  > > gyrate freely and some parts of their structure interact along the
> >  > > pulling...
> >  >
> >  > Interactions are part of the dissociation process and are not 
> > problematic per
> >  > se. But if you're trying to obtain only a one-dimensional PMF then your
> >  > rotation could be a problem. Is there some reason you need a 
> > one-dimensional
> >  > PMF and not a three-dimensional PMF? What are you trying to achieve?
> >  >
> >  > -Justin
> >  >
> >  > > Thanks a lot again for your help.
> >  > > Best wishes,
> >  > > Rebeca.
> >  > >
> >  > >
> >  > >
> >  > > 
> > 
> >  > > From: rega...@hotmail.com
> >  > > To: gmx-users@gromacs.org
> >  > > Date: Thu, 21 Jul 2011 16:36:59 +
> >  > > Subject: [gmx-users] large error bars in PMF
> >  > >
> >  > >
> >  > > Hi,
> >  > > I am trying to calculate the binding energy of two molecules using the
> >  > > PMF (Umbrella Sampling method) and Gromacs 4.0.
> >  > > Some weeks ago I have written to the list because changing the 
> > number of
> >  > > windows used in the Umbrella Sampling calculations different results
> >  > > were obtained, and I was suggested to extend my simulations since the
> >  > > error bars associated to each windows were too high.
> >  > > I have now extended my simulations from 1 ns to 8 ns, however, I 
> > cannot
> >  > > see much different from the shorter calculations. I send you the
> >  > > comparison of the two PMF including the error bars (attached).
> >  > > Now I am using 50 windows, but the shorter simulations were done using
> >  > > 100 windows, so I don't think increasing the number of windows 
> > could help.
> >  > > My system has about 29200 atoms (where 29000 are chloroform atoms). 
> > The
> >  > > *mdp file I am using is copied below.
> >  > > Would you have any suggestion to improve the results and decrease the
> >  > > error bars in the calculations?
> >  > >
> >  > > MDP file---
> >  > > title = Umbrella pulling simulation
> >  > > define =
> >  > > define =
> >  > > ; Run parameters
> >  > > integrator = md
> >  > > dt = 0.002
> >  > > tinit = 0
> >  > > nsteps = 50 ; 1 ns
> >  > > nstcomm = 10
> >  > > ; Output parameters
> >  > > nstxout = 5000 ; every 10 ps
> >  > > nstvout = 5000
> >  > > nstfout = 5000
> >  > > nstxtcout = 5000 ; every 10 ps
> >  > > nstenergy = 5000
> >  > > ; Bond parameters
> >  > > constraint_algorithm = lincs
> >  > > constraints = all-bonds
> >  > > continuation = yes
> >  > > ; Single-range cutoff scheme
> >  > > nstlist = 5
> >  > > ns_type = grid
> >  > > rlist = 1.4
> >  > > rcoulomb = 1.4
> >  > > rvdw = 1.4
> >  > 

Re: [gmx-users] large error bars in PMF

[Justin A. Lemkul]

Rebeca García Fandiño wrote:

OK,
I will try a dodecahedral box and also to extend my actual simulations.
Could you give me some advice about starting to learn about 3D PMF? I 
have not seen this in the manual, and I have never used it before. I 
have only found your tutorial about how to calculate PMF in Gromacs 4...


In practice, there's basically nothing different between 3D and 1D.  You specify 
the dimensions to which the biasing potential is applied with pull_dim or 
pull_vec (depending on the pull_geometry used).  Right now you're calculating 
the PMF along the z-dimension only ("pull_dim = N N Y"), which may be 
appropriate for one-dimensional processes or those in which the reference group 
does not rotate much in the timeframe of the sampling.  Setting "pull_dim = Y Y 
Y" will apply the restraint in all dimensions.


-Justin


Thanks a lot again for your help.
Best wishes,
Rebeca.

 > Date: Thu, 21 Jul 2011 15:16:52 -0400
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: FW: [gmx-users] large error bars in PMF
 >
 >
 >
 > Rebeca García Fandiño wrote:
 > >
 > >
 > > I am trying to achieve the binding energy of the dimer composed by the
 > > two small cyclic peptides, to compare it with experimental. What
 > > advantages would I have using 3D PMF instead only 1D for this 
calculation?

 >
 > Intuitively, two molecules diffuse through solution until they find 
one another,
 > which to me sounds a lot like a 3D path. Further, using a 
dodecahedral box for
 > your umbrella sampling removes the problems you're having with the 
peptides

 > rotating. It sounds like you're trying to pull in one direction along a
 > rectangular box, but the peptides are not playing nice. I feel like this
 > discussion has come up at least once or twice before, though...
 >
 > -Justin
 >
 > > Thanks a lot!
 > > Rebeca.
 > >
 > > > Date: Thu, 21 Jul 2011 14:14:44 -0400
 > > > From: jalem...@vt.edu
 > > > To: gmx-users@gromacs.org
 > > > Subject: Re: [gmx-users] large error bars in PMF
 > > >
 > > >
 > > >
 > > > Rebeca García Fandiño wrote:
 > > > > Hi,
 > > > > thanks a lot for your quick answer.
 > > > > What I am trying to pull are two small peptides one from 
another (r_1

 > > > > and r_2).
 > > > > I did not understand very well your last suggestion: "...if you 
want

 > > > > reasonable error bars you will not lots of well-converged data".
 > > >
 > > > Oops, that should have read "you will *need* lots of well-converged
 > > data."
 > > >
 > > > > Do you mean I will need also more windows besides extending the
 > > simulations?
 > > >
 > > > I doubt you need more windows. Likely you just need more time in 
each.

 > > >
 > > > > I think the problem could be also that the peptides I am using
 > > rotate in
 > > > > the box and they do not remain flat one respect to the other. They
 > > > > gyrate freely and some parts of their structure interact along the
 > > > > pulling...
 > > >
 > > > Interactions are part of the dissociation process and are not
 > > problematic per
 > > > se. But if you're trying to obtain only a one-dimensional PMF 
then your

 > > > rotation could be a problem. Is there some reason you need a
 > > one-dimensional
 > > > PMF and not a three-dimensional PMF? What are you trying to achieve?
 > > >
 > > > -Justin
 > > >
 > > > > Thanks a lot again for your help.
 > > > > Best wishes,
 > > > > Rebeca.
 > > > >
 > > > >
 > > > >
 > > > >
 > > 


 > > > > From: rega...@hotmail.com
 > > > > To: gmx-users@gromacs.org
 > > > > Date: Thu, 21 Jul 2011 16:36:59 +
 > > > > Subject: [gmx-users] large error bars in PMF
 > > > >
 > > > >
 > > > > Hi,
 > > > > I am trying to calculate the binding energy of two molecules 
using the

 > > > > PMF (Umbrella Sampling method) and Gromacs 4.0.
 > > > > Some weeks ago I have written to the list because changing the
 > > number of
 > > > > windows used in the Umbrella Sampling calculations different 
results
 > > > > were obtained, and I was suggested to extend my simulations 
since the

 > > > > error bars associated to each windows were too high.
 > > > > I have now extended my simulations from 1 ns to 8 ns, however, I
 > > cannot
 > > > > see much different from the shorter calculations. I send you the
 > > > > comparison of the two PMF including the error bars (attached).
 > > > > Now I am using 50 windows, but the shorter simulations were 
done using

 > > > > 100 windows, so I don't think increasing the number of windows
 > > could help.
 > > > > My system has about 29200 atoms (where 29000 are chloroform 
atoms).

 > > The
 > > > > *mdp file I am using is copied below.
 > > > > Would you have any suggestion to improve the results and 
decrease the

 > > > > error bars in the calculations?
 > > > >
 > > > > MDP file---
 > > > > title = Umbrella pulling simulation
 > > > > define =
 > > > > define =
 > > > > ; Run p

[gmx-users] ngmx

[Thomas Koller]

Hello!

Why does the animation with ngmx not work always properly?

How can I save the animation in Linux?

Thanks!
Thomas
-- 
gmx-users mailing listgmx-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

Re: [gmx-users] ngmx

[Justin A. Lemkul]

Thomas Koller wrote:

Hello!
 
Why does the animation with ngmx not work always properly?
 


You'll have to define the symptoms better to get an answer to this.  ngmx is a 
very (very) rudimentary viewing program.  You're better off with something more 
sophisticated, like VMD or PyMol.



How can I save the animation in Linux?
 


I don't think there's an option for that with ngmx.  You can export a screenshot 
in PostScript format, but there's nothing for animation.  Again, a more 
sophisticated viewer will render lovely movies for you.


-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


--
gmx-users mailing listgmx-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

Re: [gmx-users] large error bars in PMF

[XAvier Periole]

One potential problem you have is that as Justin mentioned your minimum
is not well defined and certain much less well sampled than the long  
distances

windows. Small peptides (depends the size) may sample relevant phase
space to get reasonable convergence within 8 ns when free in solution;
in contact certainly not ...

How long is you peptide?

You might get a better estimate of your error by plotting all the pmfs  
you've
got through bootstrap (if this is the case) ... and get the errors  
based on the
pmfs aligned on the long distance value and not on the "minimum" which  
is
probably what you did ... if the minimum is not well defined then it  
does not

make sense.

On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote:




Rebeca García Fandiño wrote:

OK,
I will try a dodecahedral box and also to extend my actual  
simulations.
Could you give me some advice about starting to learn about 3D PMF?  
I have not seen this in the manual, and I have never used it  
before. I have only found your tutorial about how to calculate PMF  
in Gromacs 4...


In practice, there's basically nothing different between 3D and 1D.   
You specify the dimensions to which the biasing potential is applied  
with pull_dim or pull_vec (depending on the pull_geometry used).   
Right now you're calculating the PMF along the z-dimension only  
("pull_dim = N N Y"), which may be appropriate for one-dimensional  
processes or those in which the reference group does not rotate much  
in the timeframe of the sampling.  Setting "pull_dim = Y Y Y" will  
apply the restraint in all dimensions.


-Justin


Thanks a lot again for your help.
Best wishes,
Rebeca.
> Date: Thu, 21 Jul 2011 15:16:52 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: FW: [gmx-users] large error bars in PMF
>
>
>
> Rebeca García Fandiño wrote:
> >
> >
> > I am trying to achieve the binding energy of the dimer composed  
by the

> > two small cyclic peptides, to compare it with experimental. What
> > advantages would I have using 3D PMF instead only 1D for this  
calculation?

>
> Intuitively, two molecules diffuse through solution until they  
find one another,
> which to me sounds a lot like a 3D path. Further, using a  
dodecahedral box for
> your umbrella sampling removes the problems you're having with  
the peptides
> rotating. It sounds like you're trying to pull in one direction  
along a
> rectangular box, but the peptides are not playing nice. I feel  
like this

> discussion has come up at least once or twice before, though...
>
> -Justin
>
> > Thanks a lot!
> > Rebeca.
> >
> > > Date: Thu, 21 Jul 2011 14:14:44 -0400
> > > From: jalem...@vt.edu
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] large error bars in PMF
> > >
> > >
> > >
> > > Rebeca García Fandiño wrote:
> > > > Hi,
> > > > thanks a lot for your quick answer.
> > > > What I am trying to pull are two small peptides one from  
another (r_1

> > > > and r_2).
> > > > I did not understand very well your last suggestion: "...if  
you want
> > > > reasonable error bars you will not lots of well-converged  
data".

> > >
> > > Oops, that should have read "you will *need* lots of well- 
converged

> > data."
> > >
> > > > Do you mean I will need also more windows besides extending  
the

> > simulations?
> > >
> > > I doubt you need more windows. Likely you just need more time  
in each.

> > >
> > > > I think the problem could be also that the peptides I am  
using

> > rotate in
> > > > the box and they do not remain flat one respect to the  
other. They
> > > > gyrate freely and some parts of their structure interact  
along the

> > > > pulling...
> > >
> > > Interactions are part of the dissociation process and are not
> > problematic per
> > > se. But if you're trying to obtain only a one-dimensional PMF  
then your

> > > rotation could be a problem. Is there some reason you need a
> > one-dimensional
> > > PMF and not a three-dimensional PMF? What are you trying to  
achieve?

> > >
> > > -Justin
> > >
> > > > Thanks a lot again for your help.
> > > > Best wishes,
> > > > Rebeca.
> > > >
> > > >
> > > >
> > > >
> >  


> > > > From: rega...@hotmail.com
> > > > To: gmx-users@gromacs.org
> > > > Date: Thu, 21 Jul 2011 16:36:59 +
> > > > Subject: [gmx-users] large error bars in PMF
> > > >
> > > >
> > > > Hi,
> > > > I am trying to calculate the binding energy of two  
molecules using the

> > > > PMF (Umbrella Sampling method) and Gromacs 4.0.
> > > > Some weeks ago I have written to the list because changing  
the

> > number of
> > > > windows used in the Umbrella Sampling calculations  
different results
> > > > were obtained, and I was suggested to extend my simulations  
since the

> > > > error bars associated to each windows were too high.
> > > > I have now extended my simulations from 1 ns to 8 ns,  
however, I

> > cannot
> > > > see much different from the shorter ca

RE: [gmx-users] large error bars in PMF

[Rebeca García Fandiño]

Thanks for your answer.
My peptide has 6 residues and it is cyclic.
I calculated the errors through bootstrap, using this:

g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 500 -n 
Bootstrap 200

Are the pmfs aligned on the minimum distance value? Is that the value by 
default? How could I calculate the errors based on the PMFs aligned on the long 
distance value?

Thanks a lot for all the help.

Best wishes,

Rebeca.


> From: x.peri...@rug.nl
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] large error bars in PMF
> Date: Thu, 21 Jul 2011 14:33:28 -0600
> 
> 
> One potential problem you have is that as Justin mentioned your minimum
> is not well defined and certain much less well sampled than the long  
> distances
> windows. Small peptides (depends the size) may sample relevant phase
> space to get reasonable convergence within 8 ns when free in solution;
> in contact certainly not ...
> 
> How long is you peptide?
> 
> You might get a better estimate of your error by plotting all the pmfs  
> you've
> got through bootstrap (if this is the case) ... and get the errors  
> based on the
> pmfs aligned on the long distance value and not on the "minimum" which  
> is
> probably what you did ... if the minimum is not well defined then it  
> does not
> make sense.
> 
> On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote:
> 
> >
> >
> > Rebeca García Fandiño wrote:
> >> OK,
> >> I will try a dodecahedral box and also to extend my actual  
> >> simulations.
> >> Could you give me some advice about starting to learn about 3D PMF?  
> >> I have not seen this in the manual, and I have never used it  
> >> before. I have only found your tutorial about how to calculate PMF  
> >> in Gromacs 4...
> >
> > In practice, there's basically nothing different between 3D and 1D.   
> > You specify the dimensions to which the biasing potential is applied  
> > with pull_dim or pull_vec (depending on the pull_geometry used).   
> > Right now you're calculating the PMF along the z-dimension only  
> > ("pull_dim = N N Y"), which may be appropriate for one-dimensional  
> > processes or those in which the reference group does not rotate much  
> > in the timeframe of the sampling.  Setting "pull_dim = Y Y Y" will  
> > apply the restraint in all dimensions.
> >
> > -Justin
> >
> >> Thanks a lot again for your help.
> >> Best wishes,
> >> Rebeca.
> >> > Date: Thu, 21 Jul 2011 15:16:52 -0400
> >> > From: jalem...@vt.edu
> >> > To: gmx-users@gromacs.org
> >> > Subject: Re: FW: [gmx-users] large error bars in PMF
> >> >
> >> >
> >> >
> >> > Rebeca García Fandiño wrote:
> >> > >
> >> > >
> >> > > I am trying to achieve the binding energy of the dimer composed  
> >> by the
> >> > > two small cyclic peptides, to compare it with experimental. What
> >> > > advantages would I have using 3D PMF instead only 1D for this  
> >> calculation?
> >> >
> >> > Intuitively, two molecules diffuse through solution until they  
> >> find one another,
> >> > which to me sounds a lot like a 3D path. Further, using a  
> >> dodecahedral box for
> >> > your umbrella sampling removes the problems you're having with  
> >> the peptides
> >> > rotating. It sounds like you're trying to pull in one direction  
> >> along a
> >> > rectangular box, but the peptides are not playing nice. I feel  
> >> like this
> >> > discussion has come up at least once or twice before, though...
> >> >
> >> > -Justin
> >> >
> >> > > Thanks a lot!
> >> > > Rebeca.
> >> > >
> >> > > > Date: Thu, 21 Jul 2011 14:14:44 -0400
> >> > > > From: jalem...@vt.edu
> >> > > > To: gmx-users@gromacs.org
> >> > > > Subject: Re: [gmx-users] large error bars in PMF
> >> > > >
> >> > > >
> >> > > >
> >> > > > Rebeca García Fandiño wrote:
> >> > > > > Hi,
> >> > > > > thanks a lot for your quick answer.
> >> > > > > What I am trying to pull are two small peptides one from  
> >> another (r_1
> >> > > > > and r_2).
> >> > > > > I did not understand very well your last suggestion: "...if  
> >> you want
> >> > > > > reasonable error bars you will not lots of well-converged  
> >> data".
> >> > > >
> >> > > > Oops, that should have read "you will *need* lots of well- 
> >> converged
> >> > > data."
> >> > > >
> >> > > > > Do you mean I will need also more windows besides extending  
> >> the
> >> > > simulations?
> >> > > >
> >> > > > I doubt you need more windows. Likely you just need more time  
> >> in each.
> >> > > >
> >> > > > > I think the problem could be also that the peptides I am  
> >> using
> >> > > rotate in
> >> > > > > the box and they do not remain flat one respect to the  
> >> other. They
> >> > > > > gyrate freely and some parts of their structure interact  
> >> along the
> >> > > > > pulling...
> >> > > >
> >> > > > Interactions are part of the dissociation process and are not
> >> > > problematic per
> >> > > > se. But if you're trying to obtain only a one-dimensional PMF  
> >> then your
> >> > > > rotation could be a problem. Is there some reason 

Re: [gmx-users] large error bars in PMF

[Justin A. Lemkul]

Rebeca García Fandiño wrote:

Thanks for your answer.
My peptide has 6 residues and it is cyclic.
I calculated the errors through bootstrap, using this:

g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 500 
-n Bootstrap 200


Are the pmfs aligned on the minimum distance value? Is that the value by 
default? How could I calculate the errors based on the PMFs aligned on 
the long distance value?




By default, the smallest distance along the reaction coordinate is set to an 
energy value of zero (and actually WHAM does this for each window before 
reconstructing the continuous PMF).  You can set whichever value of the reaction 
coordinate you want to take as zero with the -zprof0 option.


-Justin


Thanks a lot for all the help.

Best wishes,

Rebeca.


 > From: x.peri...@rug.nl
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] large error bars in PMF
 > Date: Thu, 21 Jul 2011 14:33:28 -0600
 >
 >
 > One potential problem you have is that as Justin mentioned your minimum
 > is not well defined and certain much less well sampled than the long
 > distances
 > windows. Small peptides (depends the size) may sample relevant phase
 > space to get reasonable convergence within 8 ns when free in solution;
 > in contact certainly not ...
 >
 > How long is you peptide?
 >
 > You might get a better estimate of your error by plotting all the pmfs
 > you've
 > got through bootstrap (if this is the case) ... and get the errors
 > based on the
 > pmfs aligned on the long distance value and not on the "minimum" which
 > is
 > probably what you did ... if the minimum is not well defined then it
 > does not
 > make sense.
 >
 > On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote:
 >
 > >
 > >
 > > Rebeca García Fandiño wrote:
 > >> OK,
 > >> I will try a dodecahedral box and also to extend my actual
 > >> simulations.
 > >> Could you give me some advice about starting to learn about 3D PMF?
 > >> I have not seen this in the manual, and I have never used it
 > >> before. I have only found your tutorial about how to calculate PMF
 > >> in Gromacs 4...
 > >
 > > In practice, there's basically nothing different between 3D and 1D.
 > > You specify the dimensions to which the biasing potential is applied
 > > with pull_dim or pull_vec (depending on the pull_geometry used).
 > > Right now you're calculating the PMF along the z-dimension only
 > > ("pull_dim = N N Y"), which may be appropriate for one-dimensional
 > > processes or those in which the reference group does not rotate much
 > > in the timeframe of the sampling. Setting "pull_dim = Y Y Y" will
 > > apply the restraint in all dimensions.
 > >
 > > -Justin
 > >
 > >> Thanks a lot again for your help.
 > >> Best wishes,
 > >> Rebeca.
 > >> > Date: Thu, 21 Jul 2011 15:16:52 -0400
 > >> > From: jalem...@vt.edu
 > >> > To: gmx-users@gromacs.org
 > >> > Subject: Re: FW: [gmx-users] large error bars in PMF
 > >> >
 > >> >
 > >> >
 > >> > Rebeca García Fandiño wrote:
 > >> > >
 > >> > >
 > >> > > I am trying to achieve the binding energy of the dimer composed
 > >> by the
 > >> > > two small cyclic peptides, to compare it with experimental. What
 > >> > > advantages would I have using 3D PMF instead only 1D for this
 > >> calculation?
 > >> >
 > >> > Intuitively, two molecules diffuse through solution until they
 > >> find one another,
 > >> > which to me sounds a lot like a 3D path. Further, using a
 > >> dodecahedral box for
 > >> > your umbrella sampling removes the problems you're having with
 > >> the peptides
 > >> > rotating. It sounds like you're trying to pull in one direction
 > >> along a
 > >> > rectangular box, but the peptides are not playing nice. I feel
 > >> like this
 > >> > discussion has come up at least once or twice before, though...
 > >> >
 > >> > -Justin
 > >> >
 > >> > > Thanks a lot!
 > >> > > Rebeca.
 > >> > >
 > >> > > > Date: Thu, 21 Jul 2011 14:14:44 -0400
 > >> > > > From: jalem...@vt.edu
 > >> > > > To: gmx-users@gromacs.org
 > >> > > > Subject: Re: [gmx-users] large error bars in PMF
 > >> > > >
 > >> > > >
 > >> > > >
 > >> > > > Rebeca García Fandiño wrote:
 > >> > > > > Hi,
 > >> > > > > thanks a lot for your quick answer.
 > >> > > > > What I am trying to pull are two small peptides one from
 > >> another (r_1
 > >> > > > > and r_2).
 > >> > > > > I did not understand very well your last suggestion: "...if
 > >> you want
 > >> > > > > reasonable error bars you will not lots of well-converged
 > >> data".
 > >> > > >
 > >> > > > Oops, that should have read "you will *need* lots of well-
 > >> converged
 > >> > > data."
 > >> > > >
 > >> > > > > Do you mean I will need also more windows besides extending
 > >> the
 > >> > > simulations?
 > >> > > >
 > >> > > > I doubt you need more windows. Likely you just need more time
 > >> in each.
 > >> > > >
 > >> > > > > I think the problem could be also that the peptides I am
 > >> using
 > >> > > rotate in
 > >> > > > > the box and they do not remain flat one respect to t

Re: [gmx-users] large error bars in PMF

[XAvier Periole]

Well I do not know how g_wham is doing but it is likely that it does  
align

different pmf obtained through the bootstraap the their minimum.

Justin just answered. The other alternative is to inverse your distances
with the data files.

On Jul 21, 2011, at 2:57 PM, Rebeca García Fandiño wrote:


Thanks for your answer.
My peptide has 6 residues and it is cyclic.
I calculated the errors through bootstrap, using this:

g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b  
500 -n Bootstrap 200


Are the pmfs aligned on the minimum distance value? Is that the  
value by default? How could I calculate the errors based on the PMFs  
aligned on the long distance value?


Thanks a lot for all the help.

Best wishes,

Rebeca.


> From: x.peri...@rug.nl
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] large error bars in PMF
> Date: Thu, 21 Jul 2011 14:33:28 -0600
>
>
> One potential problem you have is that as Justin mentioned your  
minimum

> is not well defined and certain much less well sampled than the long
> distances
> windows. Small peptides (depends the size) may sample relevant phase
> space to get reasonable convergence within 8 ns when free in  
solution;

> in contact certainly not ...
>
> How long is you peptide?
>
> You might get a better estimate of your error by plotting all the  
pmfs

> you've
> got through bootstrap (if this is the case) ... and get the errors
> based on the
> pmfs aligned on the long distance value and not on the "minimum"  
which

> is
> probably what you did ... if the minimum is not well defined then it
> does not
> make sense.
>
> On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote:
>
> >
> >
> > Rebeca García Fandiño wrote:
> >> OK,
> >> I will try a dodecahedral box and also to extend my actual
> >> simulations.
> >> Could you give me some advice about starting to learn about 3D  
PMF?

> >> I have not seen this in the manual, and I have never used it
> >> before. I have only found your tutorial about how to calculate  
PMF

> >> in Gromacs 4...
> >
> > In practice, there's basically nothing different between 3D and  
1D.
> > You specify the dimensions to which the biasing potential is  
applied

> > with pull_dim or pull_vec (depending on the pull_geometry used).
> > Right now you're calculating the PMF along the z-dimension only
> > ("pull_dim = N N Y"), which may be appropriate for one-dimensional
> > processes or those in which the reference group does not rotate  
much

> > in the timeframe of the sampling. Setting "pull_dim = Y Y Y" will
> > apply the restraint in all dimensions.
> >
> > -Justin
> >
> >> Thanks a lot again for your help.
> >> Best wishes,
> >> Rebeca.
> >> > Date: Thu, 21 Jul 2011 15:16:52 -0400
> >> > From: jalem...@vt.edu
> >> > To: gmx-users@gromacs.org
> >> > Subject: Re: FW: [gmx-users] large error bars in PMF
> >> >
> >> >
> >> >
> >> > Rebeca García Fandiño wrote:
> >> > >
> >> > >
> >> > > I am trying to achieve the binding energy of the dimer  
composed

> >> by the
> >> > > two small cyclic peptides, to compare it with experimental.  
What

> >> > > advantages would I have using 3D PMF instead only 1D for this
> >> calculation?
> >> >
> >> > Intuitively, two molecules diffuse through solution until they
> >> find one another,
> >> > which to me sounds a lot like a 3D path. Further, using a
> >> dodecahedral box for
> >> > your umbrella sampling removes the problems you're having with
> >> the peptides
> >> > rotating. It sounds like you're trying to pull in one direction
> >> along a
> >> > rectangular box, but the peptides are not playing nice. I feel
> >> like this
> >> > discussion has come up at least once or twice before, though...
> >> >
> >> > -Justin
> >> >
> >> > > Thanks a lot!
> >> > > Rebeca.
> >> > >
> >> > > > Date: Thu, 21 Jul 2011 14:14:44 -0400
> >> > > > From: jalem...@vt.edu
> >> > > > To: gmx-users@gromacs.org
> >> > > > Subject: Re: [gmx-users] large error bars in PMF
> >> > > >
> >> > > >
> >> > > >
> >> > > > Rebeca García Fandiño wrote:
> >> > > > > Hi,
> >> > > > > thanks a lot for your quick answer.
> >> > > > > What I am trying to pull are two small peptides one from
> >> another (r_1
> >> > > > > and r_2).
> >> > > > > I did not understand very well your last suggestion:  
"...if

> >> you want
> >> > > > > reasonable error bars you will not lots of well-converged
> >> data".
> >> > > >
> >> > > > Oops, that should have read "you will *need* lots of well-
> >> converged
> >> > > data."
> >> > > >
> >> > > > > Do you mean I will need also more windows besides  
extending

> >> the
> >> > > simulations?
> >> > > >
> >> > > > I doubt you need more windows. Likely you just need more  
time

> >> in each.
> >> > > >
> >> > > > > I think the problem could be also that the peptides I am
> >> using
> >> > > rotate in
> >> > > > > the box and they do not remain flat one respect to the
> >> other. They
> >> > > > > gyrate freely and some parts of their structure interact
> >> along the
> >> > > >

[gmx-users] About -chainsep and -ter

[Hsin-Lin Chiang]

Right.  Even if you somehow force pdb2gmx to write a topology in this case, the
bonds are not correct and the termini are incomplete.  That will hopefully be
resolved when the bug is fixed.  For now, you have a workaround.  Just use
"-chainsep interactive" and you will get a proper topology.

-Justin

I understand now.
Thank you very much for your help.

Sincerely yours,
Hsin-Lin
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[gmx-users] non-interactive script help

[Chandan Choudhury]

Hi gmx-users,

I was trying to feed make_ndx with the non-interactive script, below
is my command:

The script called "choice.txt" contained:
ri 1-20
ri 21-40
ri 41-60
ri 61-80
ri 81-100
ri 101-120

Initially, I used the bash shell, then csh and tcsh, but in both the
cases it failed to produce the index_1.ndx file

$make_ndx -f md20-80.tpr -o index_1.ndx < choice.txt

>
Found 162 atoms with resind.+1 in range 1-20

  5 r_1-20  :   162 atoms

>
Found 162 atoms with resind.+1 in range 21-40

  6 r_21-40 :   162 atoms

>
Found 162 atoms with resind.+1 in range 41-60

  7 r_41-60 :   162 atoms

>
Found 162 atoms with resind.+1 in range 61-80

  8 r_61-80 :   162 atoms

>
Found 162 atoms with resind.+1 in range 81-100

  9 r_81-100:   162 atoms

>
Found 162 atoms with resind.+1 in range 101-120

 10 r_101-120   :   162 atoms


---
Program make_ndx, VERSION 4.5.4
Source code file: make_ndx.c, line: 965

Fatal error:
Error reading user input
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Kindly help.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA
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Re: [gmx-users] non-interactive script help

[Terry]

You should issue a "q" command to save and quit. So "choice.txt" should look
like:

ri 1-20
...
...
ri 101-120
q


Cheers.

Terry


On Fri, Jul 22, 2011 at 1:53 PM, Chandan Choudhury wrote:

> Hi gmx-users,
>
> I was trying to feed make_ndx with the non-interactive script, below
> is my command:
>
> The script called "choice.txt" contained:
>
>> ri 1-20
>
> ri 21-40
>
> ri 41-60
>
> ri 61-80
>
> ri 81-100
>
> ri 101-120
>
>
> Initially, I used the bash shell, then csh and tcsh, but in both the
> cases it failed to produce the index_1.ndx file
>
> $make_ndx -f md20-80.tpr -o index_1.ndx < choice.txt
>
> >
> Found 162 atoms with resind.+1 in range 1-20
>
>  5 r_1-20  :   162 atoms
>
> >
> Found 162 atoms with resind.+1 in range 21-40
>
>  6 r_21-40 :   162 atoms
>
> >
> Found 162 atoms with resind.+1 in range 41-60
>
>  7 r_41-60 :   162 atoms
>
> >
> Found 162 atoms with resind.+1 in range 61-80
>
>  8 r_61-80 :   162 atoms
>
> >
> Found 162 atoms with resind.+1 in range 81-100
>
>  9 r_81-100:   162 atoms
>
> >
> Found 162 atoms with resind.+1 in range 101-120
>
>  10 r_101-120   :   162 atoms
>
>
> ---
> Program make_ndx, VERSION 4.5.4
> Source code file: make_ndx.c, line: 965
>
> Fatal error:
> Error reading user input
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> Kindly help.
>
> Chandan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] non-interactive script help

[Chandan Choudhury]

Thanks Terry.
It worked.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA



On Fri, Jul 22, 2011 at 12:00 PM, Terry  wrote:
>
> You should issue a "q" command to save and quit. So "choice.txt" should look
> like:
> ri 1-20
> ...
> ...
> ri 101-120
> q
>
> Cheers.
> Terry
>
> On Fri, Jul 22, 2011 at 1:53 PM, Chandan Choudhury 
> wrote:
>>
>> Hi gmx-users,
>>
>> I was trying to feed make_ndx with the non-interactive script, below
>> is my command:
>>
>> The script called "choice.txt" contained:
>>>
>>> ri 1-20
>>>
>>> ri 21-40
>>>
>>> ri 41-60
>>>
>>> ri 61-80
>>>
>>> ri 81-100
>>>
>>> ri 101-120
>>
>> Initially, I used the bash shell, then csh and tcsh, but in both the
>> cases it failed to produce the index_1.ndx file
>>
>> $make_ndx -f md20-80.tpr -o index_1.ndx < choice.txt
>>
>> >
>> Found 162 atoms with resind.+1 in range 1-20
>>
>>  5 r_1-20              :   162 atoms
>>
>> >
>> Found 162 atoms with resind.+1 in range 21-40
>>
>>  6 r_21-40             :   162 atoms
>>
>> >
>> Found 162 atoms with resind.+1 in range 41-60
>>
>>  7 r_41-60             :   162 atoms
>>
>> >
>> Found 162 atoms with resind.+1 in range 61-80
>>
>>  8 r_61-80             :   162 atoms
>>
>> >
>> Found 162 atoms with resind.+1 in range 81-100
>>
>>  9 r_81-100            :   162 atoms
>>
>> >
>> Found 162 atoms with resind.+1 in range 101-120
>>
>>  10 r_101-120           :   162 atoms
>>
>>
>> ---
>> Program make_ndx, VERSION 4.5.4
>> Source code file: make_ndx.c, line: 965
>>
>> Fatal error:
>> Error reading user input
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> Kindly help.
>>
>> Chandan
>>
>> --
>> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>> --
>> 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
>
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
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