Re: [gmx-users] Using mdrun -rerun to get energy values

[Martin Kamp Jensen]

Hi Mark,

On Sun, Nov 7, 2010 at 2:54 AM, Mark Abraham wrote:

>  On 7/11/2010 4:14 AM, Martin Kamp Jensen wrote:
>
> Hi Chris,
>
>  On Sat, Nov 6, 2010 at 5:58 PM, Krzysztof Mlynarczyk <
> mitomas...@gmail.com> wrote:
>
>> Hi,
>>
>> You need to use md integrator for -rerun to work.
>>
>
>  Aha, now it seems to work. Thanks!
>
>  I am just sad that I did not find that information. According to
> http://manual.gromacs.org/current/online/mdrun.html "With -rerun an input
> trajectory can be given for which forces and energies will be
> (re)calculated. Neighbor searching will be performed for every frame, unless
> nstlist is zero (see the .mdp file)."
>
>
> Writing and documenting bulletproof software is tough work :-(
>

Yes, sure - and GROMACS is not exactly a small toolset :-)


>
> I've fixed the code so that -rerun and EM or NM integrators flag a fatal
> error.
>

Great!


>
> Mark
>
>
>
>
>>
>> Good luck,
>> Chris
>>
>> 2010/11/6 Martin Kamp Jensen 
>>
>>>  Hello,
>>>
>>>  Hopefully someone can help me understand how to use the mdrun -rerun
>>> functionality, because currently I am confused. I would like to be able to
>>> look up potential energy values for a number of conformations by calling
>>> mdrun -rerun once.
>>>
>>>  The idea to use mdrun -rerun is from advice given to me by Mark Abraham
>>> on the gmx-developers list (
>>> http://lists.gromacs.org/pipermail/gmx-developers/2010-September/004731.html
>>>  and
>>> http://lists.gromacs.org/pipermail/gmx-developers/2010-October/004770.html
>>> ):
>>>
>>>  You want GROMACS to find the energy of a potentially infinite set of
 coordinates that appear magically, and that is what mdrun -rerun does.
>>>
>>>
  The elegant way to do that is to write your series of conformations to
 a pseudo-trajectory (in whichever of GROMACS many trajectory formats is
 convenient to you), and then invoke mdrun -rerun on that trajectory with a
 suitable .tpr. Then you either parse the .log file or the output .edr file
 for the energies.
>>>
>>>
>>>  I wanted to find out how this works so I have been experimenting. I
>>> started out by looking at the Peptide tutorial at
>>> http://manual.gromacs.org/current/online/speptide.html. I used three
>>> different mdp files (integrator = steep, nsteps = 0, 1, 2). This gave me
>>> three conformations and their energy values. For testing purposes I then
>>> wanted to get the energy values for those three conformations using mdrun
>>> -rerun (and since I already have the correct energy values it is easy to
>>> verify the results).
>>>
>>> First, I created a trajectory by concatenating the three conformations
>>> (gro files) into one gro file (which is okay according to
>>> http://manual.gromacs.org/current/online/gro.html: "gro files can be
>>> used as trajectory by simply concatenating files"). I then used an mdp file
>>> with integrator = steep and nsteps = 0 indicating that I just want the
>>> energy value (listed in the output, in the log file or by using g_energy).
>>> Now, by using mdrun -s  -rerun  I only get
>>> the energy value for the first conformation listed in the gro file used to
>>> create the tpr file. The -rerun option does not seem to have any effect at
>>> all.
>>>
>>>  I used the following commands three times to create three different
>>> conformations (one conf_mdrun.gro file for each time) with different energy
>>> values. I am just setting nsteps to 0, 1, or 2 (integrator = steep) in
>>> em.mdp.
>>>
>>>   pdb2gmx -f speptide -o conf_pdb2gmx -p top_pdb2gmx -i top_pdb2gmx <<
 EOF
>>>
>>>  1
>>>
>>>  1
>>>
>>>  EOF
>>>
>>>
  editconf -f conf_pdb2gmx -o conf_editconf -d 0.5
>>>
>>>
  genbox -cp conf_editconf -cs -p top_pdb2gmx -o conf_genbox
>>>
>>>  mv top_pdb2gmx.top top_genbox.top
>>>
>>>  mv "#top_pdb2gmx.top.1#" top_pdb2gmx.top
>>>
>>>
  grompp -f em -po em_grompp -c conf_genbox -p top_genbox -o em_grompp
>>>
>>>
  mdrun -s em_grompp -o mdrun -c conf_mdrun -e mdrun -g mdrun
>>>
>>>
>>>  I was hoping the following would give me the three energy values for
>>> the three conformations in 2+1+0.gro, which is the concatenation of the
>>> three conf_mdrun.gro files from before. However, I just get the energy value
>>> from the first conformation in the file. Using the -rerun option does not
>>> make a difference (I can put whatever after -rerun, even files that do not
>>> exist, without any effect).
>>>
>>>  grompp -f em -po em_grompp -c gro/2+1+0 -p top_genbox -o em_grompp
>>>
>>>
  mdrun -s em_grompp.tpr -rerun gro/2+1+0.gro
>>>
>>>
>>>  Regards,
>>> Martin.
>>>
>>>  --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
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[gmx-users] kind of contacts in protein-dna interaction during simulation

[leila karami]

Hi gromacs users



In following article, in table 2, author brings Protein–DNA contacts
observed in the simulation.

I want to know how to obtain 1) Van der Waals interactions 2) percentage of
population regarding Direct hydrogen bond, Van der Waals and Water-mediated
hydrogen bond. In method section, Protein and DNA atoms were considered
hydrogen-bonded if the distance between hydrogen and acceptor atoms was less
than 2.6 A and the donor–hydrogen–acceptor angle was greater than 120.
Hydrophobic interaction was defined when the distance between a pair of
carbon atoms was less than 4 A  Interfacial hydration water molecules were
identified by applying a cut-off 2.6 A  for the distance of water to protein
and DNA atoms simultaneously.



J. Mol. Recognit. 2004; 17: 120–131

DOI:10.1002/jmr.658



The role of flexibility and hydration on the sequence-specific DNA
recognition by the Tn916 integrase protein: a molecular dynamics analysis.


-- 

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Re: [gmx-users] kind of contacts in protein-dna interaction during simulation

[Mark Abraham]

On 7/11/2010 8:02 PM, leila karami wrote:


Hi gromacs users

In following article, in table 2, author brings Protein–DNA contacts 
observed in the simulation.


I want to know how to obtain 1) Van der Waals interactions 2) 
percentage of population regarding Direct hydrogen bond, Van der Waals 
and Water-mediated hydrogen bond. In method section, Protein and DNA 
atoms were considered hydrogen-bonded if the distance between hydrogen 
and acceptor atoms was less than 2.6 A and the donor–hydrogen–acceptor 
angle was greater than 120. Hydrophobic interaction was defined when 
the distance between a pair of carbon atoms was less than 4 A 
Interfacial hydration water molecules were identified by applying a 
cut-off 2.6 A for the distance of water to protein and DNA atoms 
simultaneously.




Take a look at section 7.4 of the manual, where it groups the tools by 
analysis type, and use that to see which tools might be useful.


Mark


J. Mol. Recognit. 2004; 17: 120–131

DOI:10.1002/jmr.658

The role of flexibility and hydration on the sequence-specific DNA 
recognition by the Tn916 integrase protein: a molecular dynamics 
analysis.




--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group



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[gmx-users] kind of contacts in protein-dna interaction during simulation

[leila karami]

Dear Mark


thanks for your attention.

I read manual before. I know that g_hbond is for hydrogen bond
analysis. But I don’t know about Van der Waals interactions analysis
and how to obtain percentage of them.

Please give me more information about what I said.


-- 

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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[gmx-users] add a group to an amino acid

[hengame fallah]

Hi,
I'm using the OPLS force field.

[ PHE ]
 [ atoms ]
 Nopls_238   -0.500 1
 Hopls_2410.300 1
CAopls_224B   0.140 1
HAopls_1400.060 1
CBopls_149   -0.005 2
   HB1opls_1400.060 2
   HB2opls_1400.060 2
CGopls_145   -0.115 2
   CD1opls_145   -0.115 3
   HD1opls_1460.115 3
   CD2opls_145   -0.115 4
   HD2opls_1460.115 4
   CE1opls_145   -0.115 5
   HE1opls_1460.115 5
   CE2opls_145   -0.115 6
   HE2opls_1460.115 6
CZopls_145   -0.115 7
HZopls_1460.115 7
 Copls_2350.500 8
 Oopls_236   -0.500 8

I want to attach "CL" atom instead of HZ
i made my pdb but when i use pdb2gmx, it adds HZ automatically in gro and
top files.
What should i do to get rid of this HZ and attach CL instead.
(I edited top and gro files and remove HZ from them, it seemed to work
properly at first, but when i tried to do energy minimization, it had errors
in top file
 and i realized that it couldn't recognized the bond between CL and CZ):

ERROR 1 [file topol.top, line 150]:
  No default Bond types


ERROR 2 [file topol.top, line 422]:
  No default Angle types


ERROR 3 [file topol.top, line 423]:
  No default Angle types

  *"topol.top":*
...
58   opls_146  3PHE HE2 22  0.115  1.008;
qtot 0.9
59   opls_145  3PHE CZ   23 -0.115 12.011   ;
qtot 0.785
60   opls_271  3PHE C 240.7 12.011 ;
qtot 1.6
61   opls_272  3PHE O1   24   -0.815.9994;
qtot 0.8
62   opls_272  3PHE O2   24   -0.815.9994;
qtot 0
63   opls_135  4EtOHCB   25  -0.18 12.011;
qtot -0.18
64   opls_140  4EtOHHB1 25   0.06  1.008 ;
qtot -0.12
65   opls_140  4EtOHHB2 25   0.06  1.008 ;
qtot -0.06
66   opls_401  5CLCL   26 -1 35.453
; qtot -1.06
...
[ bonds ]
...
  5966 1
   6061 1
   6062 1
   6364 1
   6365 1
...
[ angles ]
...
   585759 1
   555957 1
   555966 1
   575966 1
   456061 1
   456062 1
   616062 1
   646365 1
...
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[gmx-users] gpu

[Erik Wensink]

Dear gmx-users,
How to invoke the gpu for simulations, e.g. is there (compiler) flag?
Cheers,
Erik



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[gmx-users] (no subject)

[mustafa bilsel]

Hi,
when I tried to make energy minimisation,  I see following error. My
parameters are at the end of the email.  What should I do?
Fatal error:
Atomtype HW not found

Best wishes
Mustafa


MY EM.MDP
integrator= steep
nsteps=200
nstlist=10
rlist=1.0
coulombtype=pme
rcoulomb=1.0
vdw_type=cut-off
rvdw=1.0
nstenergy=10
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Re: [gmx-users] problem in executing genbox command

[ms]

On 06/11/10 07:46, Mark Abraham wrote:

On 6/11/2010 4:02 PM, bharat gupta wrote:

Hi all ,

Whenever i am running the genbox command I am getting the following
error :-


genbox -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top

:-) G R O M A C S (-:

Segmentation fault (core dumped)


The most likely scenario is some shared library is not available when it
should be. That means the environment in which you ran the above command
is different from the one in which GROMACS was built. That means
most/all GROMACS commands will fail. A possibility is that there's a bug
in GROMACS, but I doubt it. Do other GROMACS commands, or other genbox
runs work?


A missing library should show explicitly as such, not as a segfault. I 
suspect some compilation glitch. What compiler did you use? On what system?


A good idea would be to run the command through gdb.


Mark



Can anybody tell me whats the reason for such an error ...

--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 







--
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http://devicerandom.org
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[gmx-users] -b -e

[atila petrosian]

Dear gromacs users

my simulation time is 10 ns (1 ps), but, I want to use last 4ns for
analysis.

for example, if I use g_rms -b 6000 -e 1 -o rmsd.xvg, in xvg output
file, rmsd plotted versus time (from 6000 to 1 ps in horizontal axis).
while I want horizontal axis be from 0 to 4000 ps.

how to do it?
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Re: [gmx-users] -b -e

[Erik Wensink]

Hi Atila,

 You can use gmxtool trjconv to create a new trajectory file of the last 4ns. 
Or consider grace (obtain from the net) to modify the axis of your plot by hand.


--- On Sun, 11/7/10, atila petrosian  wrote:

From: atila petrosian 
Subject: [gmx-users] -b -e
To: gmx-users@gromacs.org
Date: Sunday, November 7, 2010, 2:01 PM

Dear gromacs users
 
my simulation time is 10 ns (1 ps), but, I want to use last 4ns for 
analysis. 
 
for example, if I use g_rms -b 6000 -e 1 -o rmsd.xvg, in xvg output file, 
rmsd plotted versus time (from 6000 to 1 ps in horizontal axis). while I 
want horizontal axis be from 0 to 4000 ps.
 
how to do it?
 

-Inline Attachment Follows-

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Re: [gmx-users] add a group to an amino acid

[Justin A. Lemkul]

hengame fallah wrote:

Hi,
I'm using the OPLS force field.

[ PHE ]
 [ atoms ]
 Nopls_238   -0.500 1
 Hopls_2410.300 1
CAopls_224B   0.140 1
HAopls_1400.060 1
CBopls_149   -0.005 2
   HB1opls_1400.060 2
   HB2opls_1400.060 2
CGopls_145   -0.115 2
   CD1opls_145   -0.115 3
   HD1opls_1460.115 3
   CD2opls_145   -0.115 4
   HD2opls_1460.115 4
   CE1opls_145   -0.115 5
   HE1opls_1460.115 5
   CE2opls_145   -0.115 6
   HE2opls_1460.115 6
CZopls_145   -0.115 7
HZopls_1460.115 7
 Copls_2350.500 8
 Oopls_236   -0.500 8

I want to attach "CL" atom instead of HZ
i made my pdb but when i use pdb2gmx, it adds HZ automatically in gro 
and top files.

What should i do to get rid of this HZ and attach CL instead.


If the .rtp entry says to build PHE with those constituent atoms, it will do so. 
 You can make a custom .rtp entry that has CL instead of HZ.


(I edited top and gro files and remove HZ from them, it seemed to work 
properly at first, but when i tried to do energy minimization, it had 
errors in top file

 and i realized that it couldn't recognized the bond between CL and CZ):

ERROR 1 [file topol.top, line 150]:
  No default Bond types


ERROR 2 [file topol.top, line 422]:
  No default Angle types


ERROR 3 [file topol.top, line 423]:
  No default Angle types



All of these errors indicate that OPLS cannot accommodate such a species. 
Making ad hoc changes to the topology often does this.  Look at what these lines 
contain and you will be able to identify the relevant parameters that are missing.




66   opls_401  5CLCL   26 -1 35.453 
 ; qtot -1.06


I would seriously question the validity of doing this.  Is it really correct to 
put (essentially) a Cl- ion on a Phe ring and call it correct?  Proper 
parameterization is a very challenging task, and I doubt what you've proposed 
here is valid.


http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin


...
[ bonds ]
...
  5966 1
   6061 1
   6062 1
   6364 1
   6365 1
...
[ angles ]
...
   585759 1
   555957 1
   555966 1
   575966 1
   456061 1
   456062 1
   616062 1
   646365 1
...
 



--


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] (no subject)

[Justin A. Lemkul]

mustafa bilsel wrote:

Hi,
when I tried to make energy minimisation,  I see following error. My 
parameters are at the end of the email.  What should I do?

Fatal error:
Atomtype HW not found


More pertinent information would be a description of your system, which force 
field you're using, as well as which water model you are using.  The error comes 
from a mismatch between these latter two items.  HW is a water hydrogen for most 
force fields, but the Gromos96 series use H.  I suspect you've mangled the 
topology in some way such that you've broken the internal mechanics of whatever 
force field you're using.


-Justin



Best wishes
Mustafa


MY EM.MDP
integrator= steep
nsteps=200
nstlist=10
rlist=1.0
coulombtype=pme
rcoulomb=1.0
vdw_type=cut-off
rvdw=1.0
nstenergy=10



--


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] -b -e

[Mark Abraham]

On 8/11/2010 12:01 AM, atila petrosian wrote:

Dear gromacs users
my simulation time is 10 ns (1 ps), but, I want to use last 4ns 
for analysis.
for example, if I use g_rms -b 6000 -e 1 -o rmsd.xvg, in xvg 
output file, rmsd plotted versus time (from 6000 to 1 ps in 
horizontal axis). while I want horizontal axis be from 0 to 4000 ps.

how to do it?


trjconv can be used to take subsets with -b and -e, and assign times 
with -settime. See trjconv -h.


Mark
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Re: [gmx-users] kind of contacts in protein-dna interaction during simulation

[Mark Abraham]

On 7/11/2010 9:36 PM, leila karami wrote:


Dear Mark


thanks for your attention.

I read manual before. I know that g_hbond is for hydrogen bond analysis. But I 
don’t know about Van der Waals interactions analysis and how to obtain 
percentage of them.


If you're planning to copy someone else's analysis, then you should be 
able to do so from their description. That's why they wrote the paper... 
If they don't make a description, either email them to ask, or choose 
someone else to copy :-). Unfortunately, "van der Waals interactions 
analysis" is far too vague to be a useful target question. As your email 
pointed out, there's a bunch of mathematical parameters that go into 
assigning hydrogen bonds for any analysis there...  Something similar 
would have to apply to vdW, and the procedure for finding that out will 
often lead you towards a good method for implementing it.


Mark
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Re: [gmx-users] gpu

[Rossen Apostolov]

Hi,

Did you read this? http://www.gromacs.org/gpu

Rossen

On 11/7/10 1:23 PM, Erik Wensink wrote:

Dear gmx-users,
How to invoke the gpu for simulations, e.g. is there (compiler) flag?
Cheers,
Erik




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Re: [gmx-users] gpu

[Erik Wensink]

tnx.
Erik

--- On Sun, 11/7/10, Rossen Apostolov  wrote:

From: Rossen Apostolov 
Subject: Re: [gmx-users] gpu
To: gmx-users@gromacs.org
Date: Sunday, November 7, 2010, 4:27 PM



  


  Hi,



Did you read this? http://www.gromacs.org/gpu



Rossen



On 11/7/10 1:23 PM, Erik Wensink wrote:

  
  

  
Dear gmx-users,

  How to invoke the gpu for simulations, e.g. is there
  (compiler) flag?

  Cheers,

  Erik


  

  
  




  

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[gmx-users] trjconv

[mohsen ramezanpour]

Dear Gro.users

I have a trajectory with 2 frames.
i want to separate just 1000 last frames of it in pdb formt and 1000 first
frames too.
I entered this command:
trjconv  -f  mmm.trr  -o nnn.pdb -s  lll.tpr  -b 800  -e 1000

actually my total time is 1000 ps.
the process was  not  done completely!
when I delete -e option it is done completely but the the result file is 0
byte,then i can not earn anything.
what is the problem?

thanks in advance for your comments
Mohsen
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[gmx-users] Re: trjconv

[Vitaly Chaban]

Did you try to re-run your trajectory? Does the problem persist then?



> I have a trajectory with 2 frames.
> i want to separate just 1000 last frames of it in pdb formt and 1000 first
> frames too.
> I entered this command:
> trjconv  -f  mmm.trr  -o nnn.pdb -s  lll.tpr  -b 800  -e 1000
>
> actually my total time is 1000 ps.
> the process was  not  done completely!
> when I delete -e option it is done completely but the the result file is 0
> byte,then i can not earn anything.
> what is the problem?
>
> thanks in advance for your comments
> Mohsen
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Re: [gmx-users] Re: trjconv

[Justin A. Lemkul]

Vitaly Chaban wrote:

Did you try to re-run your trajectory? Does the problem persist then?




Perhaps the faster solution would be to see what gmxcheck says about the 
trajectory.

-Justin




I have a trajectory with 2 frames.
i want to separate just 1000 last frames of it in pdb formt and 1000 first
frames too.
I entered this command:
trjconv  -f  mmm.trr  -o nnn.pdb -s  lll.tpr  -b 800  -e 1000

actually my total time is 1000 ps.
the process was  not  done completely!
when I delete -e option it is done completely but the the result file is 0
byte,then i can not earn anything.
what is the problem?

thanks in advance for your comments
Mohsen


--


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] a bug in GMXRC.bash

[Ye MEI]

Dear Gromacs developers,

I noticed that the GMXRC.bash has been updated in gromacs 4.5.2, which leads to 
a wrong manipulation to the LD_LIBRARY_PATH variable. 
The leading colon is missing, when exporting this variable for the first time.


2010-11-08 



Ye MEI 
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Re: [gmx-users] a bug in GMXRC.bash

[Roland Schulz]

This was removed for security reasons. The leading colon adds the local
directory to the list of directories searched for libraries. Why does your
setup require the colon?

Roland

On Mon, Nov 8, 2010 at 2:04 AM, Ye MEI  wrote:

>  Dear Gromacs developers,
>
> I noticed that the GMXRC.bash has been updated in gromacs 4.5.2, which
> leads to a wrong manipulation to the LD_LIBRARY_PATH variable.
> The leading colon is missing, when exporting this variable for the first
> time.
>
>
> 2010-11-08
> --
> Ye MEI
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: Re: [gmx-users] a bug in GMXRC.bash

[Ye MEI]

But later LD_LIBRARY_PATH  is redefined as 

LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH} 

without a colon between ${GMXLDLIB} and ${LD_LIBRARY_PATH} 


Ye MEI 
2010-11-08 


From: Roland Schulz 
Date: 2010-11-08  15:31:24 
To: Discussion list for GROMACS users 
CC: 
Subject: Re: [gmx-users] a bug in GMXRC.bash 
 
This was removed for security reasons. The leading colon adds the local 
directory to the list of directories searched for libraries. Why does your 
setup require the colon?


Roland


On Mon, Nov 8, 2010 at 2:04 AM, Ye MEI  wrote:

Dear Gromacs developers,

I noticed that the GMXRC.bash has been updated in gromacs 4.5.2, which leads to 
a wrong manipulation to the LD_LIBRARY_PATH variable. 
The leading colon is missing, when exporting this variable for the first time.


2010-11-08 



Ye MEI 

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Re: [gmx-users] Re: trjconv

[mohsen ramezanpour]

Dear justin

I checked what you said,yes,both of them(trr and xtc files) were completely
done as I wanted in my mdp file.

what is your points of view?

On Sun, Nov 7, 2010 at 9:15 PM, Justin A. Lemkul  wrote:

>
>
> Vitaly Chaban wrote:
>
>> Did you try to re-run your trajectory? Does the problem persist then?
>>
>>
>>
> Perhaps the faster solution would be to see what gmxcheck says about the
> trajectory.
>
> -Justin
>
>
>
>>  I have a trajectory with 2 frames.
>>> i want to separate just 1000 last frames of it in pdb formt and 1000
>>> first
>>> frames too.
>>> I entered this command:
>>> trjconv  -f  mmm.trr  -o nnn.pdb -s  lll.tpr  -b 800  -e 1000
>>>
>>> actually my total time is 1000 ps.
>>> the process was  not  done completely!
>>> when I delete -e option it is done completely but the the result file is
>>> 0
>>> byte,then i can not earn anything.
>>> what is the problem?
>>>
>>> thanks in advance for your comments
>>> Mohsen
>>>
>>
> --
> 
>
> 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] Re: trjconv

[mohsen ramezanpour]

of course I could generate a pdb file without -b and -e options,but I don't
want it.

besides I did the same process with xtc file and I resulted in a 0 byte file
:(


On Mon, Nov 8, 2010 at 11:21 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Dear justin
>
> I checked what you said,yes,both of them(trr and xtc files) were completely
> done as I wanted in my mdp file.
>
> what is your points of view?
>
>
> On Sun, Nov 7, 2010 at 9:15 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Vitaly Chaban wrote:
>>
>>> Did you try to re-run your trajectory? Does the problem persist then?
>>>
>>>
>>>
>> Perhaps the faster solution would be to see what gmxcheck says about the
>> trajectory.
>>
>> -Justin
>>
>>
>>
>>>  I have a trajectory with 2 frames.
 i want to separate just 1000 last frames of it in pdb formt and 1000
 first
 frames too.
 I entered this command:
 trjconv  -f  mmm.trr  -o nnn.pdb -s  lll.tpr  -b 800  -e 1000

 actually my total time is 1000 ps.
 the process was  not  done completely!
 when I delete -e option it is done completely but the the result file is
 0
 byte,then i can not earn anything.
 what is the problem?

 thanks in advance for your comments
 Mohsen

>>>
>> --
>> 
>>
>> 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
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
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