[gmx-users] hi questions about installing GROMACS

[Amit Choubey]

hi,
I am trying to install GROMACS (version 4.0) on my local machine. I tried to
follow the supplied simple instruction in the INSTALL file. The ./configure
step works but the "make" command doesnt work. My bash prints out  "make:
*** No targets specified and no makefile found.  Stop."

What should i do for this? Should i save the GROMACS Directory somewhere
else?


Amit
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Re: [gmx-users] Re: hi questions about installing GROMACS

[Amit Choubey]

hi,
thank you for extending the help but luckily i have figured out what was
going wrong. I have been able to install the package.

Thank you,
Amit

On Fri, Sep 4, 2009 at 1:30 PM, Vitaly V. Chaban  wrote:

> I am trying to install GROMACS (version 4.0) on my local machine. I tried
>> to
>> follow the supplied simple instruction in the INSTALL file. The
>> ./configure
>> step works but the "make" command doesnt work. My bash prints out  "make:
>> *** No targets specified and no makefile found.  Stop."
>>
>> What should i do for this? Should i save the GROMACS Directory somewhere
>> else?
>>
>>
> Hi,
>
> What does your configure script finish with?
>
>
> --
> Vitaly V. Chaban, Ph.D. (ABD)
> School of Chemistry
> V.N. Karazin Kharkiv National University
> Svoboda sq.,4, Kharkiv 61077, Ukraine
> email: cha...@univer.kharkov.ua,vvcha...@gmail.com
> skype: vvchaban, cell.: +38-097-8259698
> http://www-rmn.univer.kharkov.ua/chaban.html
> ===
> !!! Looking for a postdoctoral position !!!
> ===
>
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[gmx-users] how to use a new force field

[Amit Choubey]

hi gromacs user,
Is there any good way to introduce new force field in the gromacs library?

Amit
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Re: [gmx-users] how to use a new force field

[Amit Choubey]

Hi,

so is it a good idea to edit the original gromacs files in top directory for
introducing new force field or is there a way to compliment the existing FF
files by a new file made by me?

Amit

On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> hi gromacs user,
>>
>> Is there any good way to introduce new force field in the gromacs library?
>>
>>
> Read in the manual about the organization of existing force fields, as well
> as the component files that are necessary to make it function.  Beyond that,
> look at the implemented force fields themselves and see how they work
> together.
>
> -Justin
>
>  Amit
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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] how to use a new force field

[Amit Choubey]

hi,
ok the next question that bugs me is if i make a directory consisting of my
modified force field (*.atp, *.rtp, *bon.itp,*nb.itp) and i want to use
pdb2gmx to get the *.top & .gro files according to the above new FF files,
how do i supply this info to pdb2gmx. In other words how do i make pdb2gmx
aware of the new FF files.

Amit

On Tue, Sep 8, 2009 at 6:58 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi,
>>
>> so is it a good idea to edit the original gromacs files in top directory
>> for introducing new force field or is there a way to compliment the existing
>> FF files by a new file made by me?
>>
>
> It is generally better to not mess with system-level force field files
> unless you're very sure of what you're doing, and experienced in making such
> changes. If you alter one of the original force field files, and you don't
> do it right, reverting the changes is often difficult.  If, for example, you
> want to modify the OPLS-AA force field, do not ever make any changes to the
> original file, instead implement them in files like ffoplsaa_mod.*
>
> It is even safer to implement your changes in the local directory until you
> are confident everything is working properly, then if you're comfortable
> that you've done everything 100% right, move your files into /share/top for
> convenience later.
>
> -Justin
>
>
>> Amit
>>
>> On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>hi gromacs user,
>>
>>Is there any good way to introduce new force field in the
>>gromacs library?
>>
>>
>>Read in the manual about the organization of existing force fields,
>>as well as the component files that are necessary to make it
>>function.  Beyond that, look at the implemented force fields
>>themselves and see how they work together.
>>
>>-Justin
>>
>>Amit
>>
>>
>>  
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
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>><mailto:gmx-users-requ...@gromacs.org>.
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>>
>>
>>--
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>___
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>><mailto:gmx-users@gromacs.org>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
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>><mailto:gmx-users-requ...@gromacs.org>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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] how to use a new force field

[Amit Choubey]

By the way thank you very much for answering my questions.

Amit

On Tue, Sep 8, 2009 at 7:13 PM, Amit Choubey  wrote:

> hi,
> ok the next question that bugs me is if i make a directory consisting of my
> modified force field (*.atp, *.rtp, *bon.itp,*nb.itp) and i want to use
> pdb2gmx to get the *.top & .gro files according to the above new FF files,
> how do i supply this info to pdb2gmx. In other words how do i make pdb2gmx
> aware of the new FF files.
>
> Amit
>
>
> On Tue, Sep 8, 2009 at 6:58 PM, Justin A. Lemkul  wrote:
>
>>
>>
>> Amit Choubey wrote:
>>
>>> Hi,
>>>
>>> so is it a good idea to edit the original gromacs files in top directory
>>> for introducing new force field or is there a way to compliment the existing
>>> FF files by a new file made by me?
>>>
>>
>> It is generally better to not mess with system-level force field files
>> unless you're very sure of what you're doing, and experienced in making such
>> changes. If you alter one of the original force field files, and you don't
>> do it right, reverting the changes is often difficult.  If, for example, you
>> want to modify the OPLS-AA force field, do not ever make any changes to the
>> original file, instead implement them in files like ffoplsaa_mod.*
>>
>> It is even safer to implement your changes in the local directory until
>> you are confident everything is working properly, then if you're comfortable
>> that you've done everything 100% right, move your files into /share/top for
>> convenience later.
>>
>> -Justin
>>
>>
>>> Amit
>>>
>>> On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>Amit Choubey wrote:
>>>
>>>hi gromacs user,
>>>
>>>Is there any good way to introduce new force field in the
>>>gromacs library?
>>>
>>>
>>>Read in the manual about the organization of existing force fields,
>>>as well as the component files that are necessary to make it
>>>function.  Beyond that, look at the implemented force fields
>>>themselves and see how they work together.
>>>
>>>-Justin
>>>
>>>Amit
>>>
>>>
>>>  
>>>
>>>___
>>>gmx-users mailing listgmx-users@gromacs.org
>>><mailto:gmx-users@gromacs.org>
>>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at http://www.gromacs.org/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
>>><mailto:gmx-users-requ...@gromacs.org>.
>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>--
>>>
>>>Justin A. Lemkul
>>>Ph.D. Candidate
>>>ICTAS Doctoral Scholar
>>>Department of Biochemistry
>>>Virginia Tech
>>>Blacksburg, VA
>>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>
>>>___
>>>gmx-users mailing listgmx-users@gromacs.org
>>><mailto:gmx-users@gromacs.org>
>>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at http://www.gromacs.org/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
>>><mailto:gmx-users-requ...@gromacs.org>.
>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> 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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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>
>
>
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Re: [gmx-users] how to use a new force field

[Amit Choubey]

Thank you v. much for the replies. I will try to set that up.

Amit

On Tue, Sep 8, 2009 at 6:57 PM, Dallas B. Warren <
dallas.war...@pharm.monash.edu.au> wrote:

> Best if you don't mess with the ones that are installed.  Set up your own
> forcefield files in a local directory and edit those, GROMACS scripts will
> then look in the local directory first, before going to the installed one.
>
> Catch ya,
>
> Dr. Dallas Warren
> Department of Pharmaceutical Biology
> Pharmacy and Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.war...@pharm.monash.edu.au
> +61 3 9903 9167
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of Amit Choubey
> Sent: Wednesday, 9 September 2009 11:53 AM
> To: jalem...@vt.edu; Discussion list for GROMACS users
> Subject: Re: [gmx-users] how to use a new force field
>
> Hi,
>
> so is it a good idea to edit the original gromacs files in top directory
> for introducing new force field or is there a way to compliment the existing
> FF files by a new file made by me?
>
> Amit
>
> On Tue, Sep 8, 2009 at 2:38 PM, Justin A. Lemkul  wrote:
>
>
> Amit Choubey wrote:
> hi gromacs user,
>
> Is there any good way to introduce new force field in the gromacs library?
>
> Read in the manual about the organization of existing force fields, as well
> as the component files that are necessary to make it function.  Beyond that,
> look at the implemented force fields themselves and see how they work
> together.
>
> -Justin
> Amit
>
> 
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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] bypassing pdb2gmx

[Amit Choubey]

hi everyone,
I have a pdb file of my system and i want it to be fed into the GROMACS
software. I have a new force field for the simulation and i have made the
.top file manually which includes the new library FF files. I need to get a
.gro file from the .pdb file that i have. So, is there a way out to do this
without incorporating pdb2gmx because i dont use the standard FF and i dont
really have all the other datafiles for the new FF except for necessary bond
and nonbonded infos.

Amit
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[gmx-users] pdb2gmx question

[Amit Choubey]

hi everyone,
I am trying to set up a very small simulation with DPPC lipid. I am using
the GROMOS96 53a6 FF. Now i have my pdb file which looks like

ATOM  1  C33  DPPC1  15.771  52.651   9.201  1.00  0.00
ATOM  2  C34  DPPC1  16.750  52.953  11.353  1.00  0.00
ATOM  3  C35  DPPC1  16.477  54.817   9.854  1.00  0.00
ATOM  4  NDPPC1  16.796  53.384   9.947  1.00  0.00
ATOM  5  C32  DPPC1  18.082  53.008   9.318  1.00  0.00
ATOM  6  C31  DPPC1  19.292  53.957   9.530  1.00  0.00
ATOM  7  O32  DPPC1  19.653  54.093  10.906  1.00  0.00
ATOM  8  PDPPC1  20.931  54.971  11.160  1.00  0.00
ATOM  9  O33  DPPC1  21.965  54.328  10.317  1.00  0.00
ATOM 10  O34  DPPC1  20.513  56.372  10.957  1.00  0.00
ATOM 11  O31  DPPC1  21.096  54.572  12.688  1.00  0.00
ATOM 12  C3   DPPC1  20.436  55.317  13.711  1.00  0.00
ATOM 13  C2   DPPC1  20.715  54.687  15.095  1.00  0.00
ATOM 14  O21  DPPC1  20.250  55.525  16.189  1.00  0.00
ATOM 15  C21  DPPC1  18.977  55.438  16.644  1.00  0.00
ATOM 16  O22  DPPC1  18.253  54.474  16.407  1.00  0.00
ATOM 17  C22  DPPC1  18.585  56.603  17.549  1.00  0.00
ATOM 18  C23  DPPC1  17.728  56.214  18.751  1.00  0.00
ATOM 19  C24  DPPC1  17.396  57.481  19.541  1.00  0.00
ATOM 20  C25  DPPC1  16.456  57.200  20.713  1.00  0.00
ATOM 21  C26  DPPC1  16.196  58.488  21.496  1.00  0.00
ATOM 22  C27  DPPC1  15.247  58.258  22.678  1.00  0.00
ATOM 23  C28  DPPC1  15.849  57.273  23.685  1.00  0.00
ATOM 24  C29  DPPC1  14.863  56.871  24.797  1.00  0.00
ATOM 25  C210 DPPC1  15.354  55.818  25.560  1.00  0.00
ATOM 26  C211 DPPC1  14.405  55.341  26.675  1.00  0.00

Now for atoms C210, C211 etc (with three no. after the element name) the
pdb2gmx prints out following kind of warning

WARNING: atom C210 is missing in residue DPP 1 in the pdb file


WARNING: atom C211 is missing in residue DPP 1 in the pdb file

I am sure that it has to do with the way i am writing the pdb file (ie
format) . I am sure that the pdb2gmx is actually detecting the right kind of
molecule (DPPC) . But i cannot figure out how exactly to write my pdb file.

Thank you in advance
Amit
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[gmx-users] Re: bypassing pdb2gmx

[Amit Choubey]

hi everyone,
I guess if i knew the exact format of .gro files i could write a small code
to copy data from pdb to gro . I cannot find this info anywhere. I believe
that it has co-ordinates and velocities but how are the velocities choose
(randomly?). I am also not sure abt the exact order.

Amit

On Wed, Sep 9, 2009 at 5:29 PM, Amit Choubey  wrote:

> hi everyone,
> I have a pdb file of my system and i want it to be fed into the GROMACS
> software. I have a new force field for the simulation and i have made the
> .top file manually which includes the new library FF files. I need to get a
> .gro file from the .pdb file that i have. So, is there a way out to do this
> without incorporating pdb2gmx because i dont use the standard FF and i dont
> really have all the other datafiles for the new FF except for necessary bond
> and nonbonded infos.
>
> Amit
>
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Re: [gmx-users] Re: bypassing pdb2gmx

[Amit Choubey]

thanks a bunch for the input.

On Thu, Sep 10, 2009 at 9:38 AM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> hi everyone,
>>
>> I guess if i knew the exact format of .gro files i could write a small
>> code to copy data from pdb to gro . I cannot find this info anywhere. I
>> believe that it has co-ordinates and velocities but how are the velocities
>> choose (randomly?). I am also not sure abt the exact order.
>>
>>
> The format is available as part of the online manual:
>
> http://manual.gromacs.org/current/online/gro.html
>
> Although I don't know why you feel it necessary to write code that's
> already part of editconf.
>
> Velocities are assigned randomly when grompp sees "gen_vel = yes" in the
> .mdp file, according to the gen_temp parameter.  I'd say keep life easy and
> use the functions Gromacs already provides you instead of writing code for
> converting coordinates and writing velocities :)
>
> -Justin
>
>  Amit
>>
>> On Wed, Sep 9, 2009 at 5:29 PM, Amit Choubey > kgp.a...@gmail.com>> wrote:
>>
>>hi everyone,
>>
>>I have a pdb file of my system and i want it to be fed into the
>>GROMACS software. I have a new force field for the simulation and i
>>have made the .top file manually which includes the new library FF
>>files. I need to get a .gro file from the .pdb file that i have. So,
>>is there a way out to do this without incorporating pdb2gmx because
>>i dont use the standard FF and i dont really have all the other
>>datafiles for the new FF except for necessary bond and nonbonded infos.
>>
>>Amit
>>
>>
>>
>> 
>>
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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] mpi version of gromacs

[Amit Choubey]

Hi everyone,
I have the gromacs mpi version on my system and everything in the simulation
works fine until i get to mdrun_mpi and when i use this executable the
following pops error comes up

MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX device entry in
/dev.

Then i tried the to do mdrun_mpi -h on the terminal and the same thing comes
out.

MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX device entry in
/dev.

Is this an installation problem? I am also not able to find the online
manual for mpi version of gromacs, could someone send me the link?

Thank you,
Amit
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Re: [gmx-users] mpi version of gromacs

[Amit Choubey]

ok here the pbs file for the job
#!/bin/bash
#PBS -l nodes=1:ppn=1
#PBS -l walltime=00:01:59
#PBS -o output.out
#PBS -j oe
#PBS -N mdrun
WORK_HOME=/auto/hpc-08/knomura/choubey/GROMACS/test
cd $WORK_HOME
source /usr/usc/mpich/default/setup.sh
mdrun_mpi -v -s em -o em -c after_em -g emlog

Is my command line wrong?

On Tue, Sep 15, 2009 at 6:25 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi everyone,
>>
>> I have the gromacs mpi version on my system and everything in the
>> simulation works fine until i get to mdrun_mpi and when i use this
>> executable the following pops error comes up
>>
>> MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX device entry
>> in /dev.
>>
>> Then i tried the to do mdrun_mpi -h on the terminal and the same thing
>> comes out.
>>
>> MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX device entry
>> in /dev.
>>
>> Is this an installation problem? I am also not able to find the online
>> manual for mpi version of gromacs, could someone send me the link?
>>
>>
> Because MPI only applies to mdrun, so there's no need for a separate
> manual. All the information for mdrun applies to mdrun_mpi, except that it
> can be executed in parallel.
>
> It looks like there is either a problem with the MPI implementation of the
> machine, or you're calling the command wrong.  If you can post your command
> line or the contents of whatever submission script you might be using, we
> might be able to implicate (or rule out) the latter.
>
> -Justin
>
>  Thank you,
>> Amit
>>
>> 
>>
>> ___
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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] analyzing gromacs trajectories on VMD

[Amit Choubey]

hi everyone,
I want to analyze the gromacs trajectories using vmd, is there a quick way
of doing so ? Is there a reference for this?

Thank you
Amit
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[gmx-users] question about chain identifier

[Amit Choubey]

hi everyone,
I had a question about the purpose of chain identifier character in pdb.
What does it mean for Gromacs, i mean what does gromacs do with it? I
actually have a "bad" pdb file which has *different* chain identifiers for
first few molecules of the same type and then there exists none for rest of
the molecules (I am dealing with only one kind of molecule). The limitation
is due to the fact that the chain identifier has to be a single character.
Now the molecules are also distinguished by there residue sequence no. in
the pdb file, which makes the purpose of chain identifier useless.

So should i get rid of all the chain identifiers in the pdb file?

I am also interested in knowing what the chain identifier really does?

Thank you,
Amit
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[gmx-users] using 'genbox' for adding solvent

[Amit Choubey]

Hi everyone,
I have been trying to insert a fixed no. of water molecules in my system. I
first tried the -cp -cs options and could insert some water molecules. But I
still need to insert  few more water molecules and for that i tried using
the -nmol -ci option. I made a file named "insert.gro" which has a single
water molecule with the right volume associated with it.
But this option gave a segmentation fault and i am not sure why its doing
that? May be there's not enough space for additional water but it should not
give a segmentation fault for that reason. Is there something wrong with my
idea?

The insert.gro looks like the following

H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984
  3
1SOL OW1.130.128.113
1SOLHW12.037.126.150
1SOLHW23.131.089.021
   0.31034   0.31034   0.31034

I also tried various other box (larger) sizes for this but it didnt help.

Thank you in advance.

Amit
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Re: [gmx-users] using 'genbox' for adding solvent

[Amit Choubey]

I still want to suggest that segmentation fault doesn't occur due to large
no. of insertion molecules the reason being that i, once tried to insert
only 1 molecule and it came up with seg. fault again . I am very sure that i
have space for atleast some(>1) no. of water molecules.
Amit

On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi everyone,
>>
>> I have been trying to insert a fixed no. of water molecules in my system.
>> I first tried the -cp -cs options and could insert some water molecules. But
>> I still need to insert  few more water molecules and for that i tried using
>> the -nmol -ci option. I made a file named "insert.gro" which has a single
>> water molecule with the right volume associated with it. But this option
>> gave a segmentation fault and i am not sure why its doing that? May be
>> there's not enough space for additional water but it should not give a
>> segmentation fault for that reason. Is there something wrong with my idea?
>>
>>
> A segmentation fault with this approach generally indicates that the
> requested number of inserted molecules will not fit.
>
> Alternately, you can try -cs spc216.gro -maxsol (your number)
>
> If the second approach also fails, I would think that would be strong
> evidence that what you're trying to do won't work.
>
> -Justin
>
>  The insert.gro looks like the following
>>
>> H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984
>>  3
>>1SOL OW1.130.128.113
>>1SOLHW12.037.126.150
>>1SOLHW23.131.089.021
>>   0.31034   0.31034   0.31034
>>
>> I also tried various other box (larger) sizes for this but it didnt help.
>> Thank you in advance.
>>
>> Amit
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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] using 'genbox' for adding solvent

[Amit Choubey]

yes you are right its a bug, everything works well on the most recent
version.
Thank you

On Sun, Sep 20, 2009 at 6:55 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> I still want to suggest that segmentation fault doesn't occur due to large
>> no. of insertion molecules the reason being that i, once tried to insert
>> only 1 molecule and it came up with seg. fault again . I am very sure that i
>> have space for atleast some(>1) no. of water molecules.
>>
>>
> Which version of Gromacs are you using?  There was a bug in genbox 4.0.3,
> but was fixed prior to 4.0.4.
>
> -Justin
>
>  Amit
>>
>>
>> On Sun, Sep 20, 2009 at 6:38 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>Hi everyone,
>>
>>I have been trying to insert a fixed no. of water molecules in
>>my system. I first tried the -cp -cs options and could insert
>>some water molecules. But I still need to insert  few more water
>>molecules and for that i tried using the -nmol -ci option. I
>>made a file named "insert.gro" which has a single water molecule
>>with the right volume associated with it. But this option gave a
>>segmentation fault and i am not sure why its doing that? May be
>>there's not enough space for additional water but it should not
>>give a segmentation fault for that reason. Is there something
>>wrong with my idea?
>>
>>
>>A segmentation fault with this approach generally indicates that the
>>requested number of inserted molecules will not fit.
>>
>>Alternately, you can try -cs spc216.gro -maxsol (your number)
>>
>>If the second approach also fails, I would think that would be
>>strong evidence that what you're trying to do won't work.
>>
>>-Justin
>>
>>The insert.gro looks like the following
>>
>>H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=0.31034NM,WFVG,MAR. 1984
>> 3
>>   1SOL OW1.130.128.113
>>   1SOLHW12.037.126.150
>>   1SOLHW23.131.089.021
>>  0.31034   0.31034   0.31034
>>
>>I also tried various other box (larger) sizes for this but it
>>didnt help.
>>Thank you in advance.
>>
>>Amit
>>
>>
>>
>>  
>>
>>___
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>><mailto:gmx-users@gromacs.org>
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>>
>>
>>--
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
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>>posting!
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>>
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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] question about energy minimization

[Amit Choubey]

Hi everyone,
I recently was doing a simulation where i had inserted water into the system
forcefully( using -ci -nmol option of the genbox). I didnt change the box
dimensions after the insertion of the extra molecules. Then i did energy
minimization on the system and somehow it moved the atoms out of the box
(some co-ordinates became negative and some became more than the box size).
I did not want the program to do this i would have rather removed some of
the molecules. Is there a way to control this? Interestingly, the energy
minimization log didnt show any of the above changes, it also didnt change
the box size in its output gro file?

I actually didnt realize this until i did a long simulation after which the
trajectories of some of the atoms looked way out of the box dimensions. The
co-ordinates of many atoms didnt lie in the box range. Although the output
file contained the same box dimensions as I started with. Could someone help
me in understanding what happened?

Thank you,
Amit Choubey
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Re: [gmx-users] question about energy minimization

[Amit Choubey]

Hi Omer,

My question was to how to avoid the "diffusion" of molecules out of the box
during energy minimization and MD  run? I think what you suggested here will
just change the present trajectory into a new by using the pbc condition.

But i am wondering shouldnt this be done in MD calculation itself. It seems
me to me that physics will be significantly different if i dont put the
particles which go out of the box, back into the box. In that way the box
will keep on expanding as i increase my simulation time and the calculated
equilibirium properties wont be very meaningful and will fluctuate more than
they really should.

By the way i am talking about long chain lipid molecules here and i am using
an all bond constraint.

Amit



On Tue, Sep 29, 2009 at 5:17 AM, Omer Markovitch  wrote:

> Trj "trjconv -pbc nojump", or "trjconv -h" and read the short help printed.
> Omer.
>
>
>>
>> I actually didnt realize this until i did a long simulation after which
>> the trajectories of some of the atoms looked way out of the box dimensions.
>> The co-ordinates of many atoms didnt lie in the box range. Although the
>> output file contained the same box dimensions as I started with. Could
>> someone help me in understanding what happened?
>>
>>
>
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Re: [gmx-users] Problem: Protein move out of box

[Amit Choubey]

you can use trjconv -pbc nojump to take care of that.



On 10/8/09, Pan Wu  wrote:
> Hi Gromacs users,I am new to Gromacs, and now setting up one very simple
> system to test Gromacs+Martini. (one protein with solvent surrounded)
> When I run the MD and saw the trajectory, the protein seems go around
> randomly, and across the box size. Because Periodic Boundary Condition, it
> will come back from the other side. But I don't know *whether the across box
> size movement will actually cause some problem about protein structure or
> dynamics*?
>
> In my mdout.mdp file, I can see:
> comm-mode = Linear
> nstcomm = 1
> comm-grps  =  (default, should be system)
>
> Thank you in advance!
>
> Sincerely
> Pan
>
>
>
> --
> Sincerely
> =
> Pan Wu
> Graduate Student in Department of Chemistry
> Duke University
> 124 Science Drive
> 5301 French Family Science Center
> Durham, NC 27708
> Phone: (919) 660-1583
> =
>
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[gmx-users] increasing the system size

[Amit Choubey]

Hi everyone,

I was looking for ways to increase the system size (no. of atoms)
beyond 9 . I read somewhere that there is no inherent constraint
in gromacs on system size rather its because of the format of .gro . I
cant find where i read this but could someone suggest me what to do if
i need to go beyond 9.

thank you,
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[gmx-users] creating a larger lipid membrane

[Amit Choubey]

Dear Gromacs Users,
I have been trying to generate a larger lipid system but am running into
troubles due to improper initial co-ordinates set up. Following are the
steps i am trying to follow.

1. I start with a 128 dppc membrane and use genconf to create a larger
system. I got the dppc128.pdb from Dr. Peter Tieleman's website.

2. I changed my topology file accordingly (change the number of DPPC and
Water molecules)

3. I move on to energy minimization. During the mdrun i see the following
message :-

Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which is
larger than the 1-4 table size 2.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

I also notice that the max force does not converge to less than 2000 rather
its of the order of 2e+06 .

4. I tried to do energy minimization again on the above system but the
steepest descent could not change the potential energy substantially and
terminated after less that 20 steps. I again noticed the following warning

Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which is
larger than the 1-4 table size 2.800 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc =
xyz has been used as default.

Same warnings were printed out during energy minimization.

6. I also tried to use the table-extension option and increased its value to
10 nm but later the LINCS printed out too many warnings and MD could not be
done. I know that its not at all a good idea to increase the 1-4 cut off.

By the way to be specific the system size was 12 x 12 x 6 in nm3. I had 256
lipids and about 7300 water molecules.


I believe that this might not be the best way to create a larger bilayer
system. Could somebody suggest me other ways of doing this?

Any help will be appreciated thank you

Amit
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Re: [gmx-users] creating a larger lipid membrane

[Amit Choubey]

Hi Justin,
Yes you are right. I didnt fix the periodicity to start with. Could you tell
me how to do that, which command to work with?
Thanks.

amit

On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Dear Gromacs Users,
>>
>> I have been trying to generate a larger lipid system but am running into
>> troubles due to improper initial co-ordinates set up. Following are the
>> steps i am trying to follow.
>>
>> 1. I start with a 128 dppc membrane and use genconf to create a larger
>> system. I got the dppc128.pdb from Dr. Peter Tieleman's website.
>>
>>
> Did you correct for periodicity before you extended the system?  The files
> distributed by Tieleman are compact representations.
>
>  2. I changed my topology file accordingly (change the number of DPPC and
>> Water molecules)
>>
>> 3. I move on to energy minimization. During the mdrun i see the following
>> message :-
>>
>> Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which is
>> larger than the 1-4 table size 2.800 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>>
>>
> Looks to me like two bonded atoms are across the box from each other, which
> seems to answer my question above :)
>
>  I also notice that the max force does not converge to less than 2000
>> rather its of the order of 2e+06 .
>>
>> 4. I tried to do energy minimization again on the above system but the
>> steepest descent could not change the potential energy substantially and
>> terminated after less that 20 steps. I again noticed the following warning
>> Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which is
>> larger than the 1-4 table size 2.800 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>>
>> 5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc =
>> xyz has been used as default.
>>
>>
> Bad idea.  This option is for "infinite" molecules, like nanotubes or
> graphene sheets that are supposed to extend across the simulation box.
>
>  Same warnings were printed out during energy minimization.
>>
>> 6. I also tried to use the table-extension option and increased its value
>> to 10 nm but later the LINCS printed out too many warnings and MD could not
>> be done. I know that its not at all a good idea to increase the 1-4 cut off.
>>
>>
> The standard advice is to fix the problem with the system, not change the
> table-extension.
>
>  By the way to be specific the system size was 12 x 12 x 6 in nm3. I had
>> 256 lipids and about 7300 water molecules.
>>
>> I believe that this might not be the best way to create a larger bilayer
>> system. Could somebody suggest me other ways of doing this?
>>
>>
> Fix periodicity, then use genconf.
>
> -Justin
>
>  Any help will be appreciated thank you
>>
>> Amit
>>
>>
>>
>> 
>>
>> ___
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>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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] creating a larger lipid membrane

[Amit Choubey]

Hi Mark,
Yes i checked the procedure on the original structure. It woks fine. As for
genconf i used the following

genconf -f dppc128.pdb -o out.gro -nbox 2 2 1

As Justin pointed out, I did not correct the periodicity of original
structure before using genconf .

Thank you,
Amit

On Fri, Oct 9, 2009 at 5:44 PM, Mark Abraham wrote:

> Amit Choubey wrote:
>
>> Dear Gromacs Users,
>>
>> I have been trying to generate a larger lipid system but am running into
>> troubles due to improper initial co-ordinates set up. Following are the
>> steps i am trying to follow.
>>
>> 1. I start with a 128 dppc membrane and use genconf to create a larger
>> system. I got the dppc128.pdb from Dr. Peter Tieleman's website.
>>
>
> What command line did you use?
>
>  2. I changed my topology file accordingly (change the number of DPPC and
>> Water molecules)
>>
>> 3. I move on to energy minimization. During the mdrun i see the following
>> message :-
>>
>
> Test your protocol on the original coordinate file. It needs to work for
>  your procedure to be sound.
>
>  Warning: 1-4 interaction between 1854 and 1857 at distance 6.249 which is
>> larger than the 1-4 table size 2.800 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>>
>> I also notice that the max force does not converge to less than 2000
>> rather its of the order of 2e+06 .
>>
>> 4. I tried to do energy minimization again on the above system but the
>> steepest descent could not change the potential energy substantially and
>> terminated after less that 20 steps. I again noticed the following warning
>> Warning: 1-4 interaction between 1854 and 1857 at distance 5.269 which is
>> larger than the 1-4 table size 2.800 nm
>> These are ignored for the rest of the simulation
>> This usually means your system is exploding,
>> if not, you should increase table-extension in your mdp file
>> or with user tables increase the table size
>>
>> 5. Now i changed my mdp files to do periodic_molecules = yes . Note pbc =
>> xyz has been used as default.
>>
>> Same warnings were printed out during energy minimization.
>>
>
> You don't have periodic molecules. Changing mdp options haphazardly is a
> recipe for problems. Read 7.3 about them in the first instance, and then
> look up in the table of contents for more background.
>
>  6. I also tried to use the table-extension option and increased its value
>> to 10 nm but later the LINCS printed out too many warnings and MD could not
>> be done. I know that its not at all a good idea to increase the 1-4 cut off.
>>
>
> Yup, bad idea. Fix the underlying problem, not the symptoms.
>
> Mark
>
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Re: [gmx-users] creating a larger lipid membrane

[Amit Choubey]

Thank you for the tip. I will try to use it.
Amit

On Fri, Oct 9, 2009 at 6:10 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi Justin,
>>
>> Yes you are right. I didnt fix the periodicity to start with. Could you
>> tell me how to do that, which command to work with?
>> Thanks.
>>
>>
> Periodicity is corrected using trjconv.  This involves creating a .tpr file
> of to represent the system and using trjconv -pbc mol -ur compact, or some
> such equivalent.
>
> My tutorial gives some information on doing this.  Please see:
>
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
>
> -Justin
>
>  amit
>>
>>
>> On Fri, Oct 9, 2009 at 5:39 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>Dear Gromacs Users,
>>
>>I have been trying to generate a larger lipid system but am
>>running into troubles due to improper initial co-ordinates set
>>up. Following are the steps i am trying to follow.
>>
>>1. I start with a 128 dppc membrane and use genconf to create a
>>larger system. I got the dppc128.pdb from Dr. Peter Tieleman's
>>website.
>>
>>
>>Did you correct for periodicity before you extended the system?  The
>>files distributed by Tieleman are compact representations.
>>
>>
>>2. I changed my topology file accordingly (change the number of
>>DPPC and Water molecules)
>>
>>3. I move on to energy minimization. During the mdrun i see the
>>following message :-
>>
>>Warning: 1-4 interaction between 1854 and 1857 at distance 6.249
>>which is larger than the 1-4 table size 2.800 nm
>>These are ignored for the rest of the simulation
>>This usually means your system is exploding,
>>if not, you should increase table-extension in your mdp file
>>or with user tables increase the table size
>>
>>
>>Looks to me like two bonded atoms are across the box from each
>>other, which seems to answer my question above :)
>>
>>
>>I also notice that the max force does not converge to less than
>>2000 rather its of the order of 2e+06 .
>>
>>4. I tried to do energy minimization again on the above system
>>but the steepest descent could not change the potential energy
>>substantially and terminated after less that 20 steps. I again
>>noticed the following warning
>>Warning: 1-4 interaction between 1854 and 1857 at distance 5.269
>>which is larger than the 1-4 table size 2.800 nm
>>These are ignored for the rest of the simulation
>>This usually means your system is exploding,
>>if not, you should increase table-extension in your mdp file
>>or with user tables increase the table size
>>
>>5. Now i changed my mdp files to do periodic_molecules = yes .
>>Note pbc = xyz has been used as default.
>>
>>
>>Bad idea.  This option is for "infinite" molecules, like nanotubes
>>or graphene sheets that are supposed to extend across the simulation
>>box.
>>
>>
>>Same warnings were printed out during energy minimization.
>>
>>6. I also tried to use the table-extension option and increased
>>its value to 10 nm but later the LINCS printed out too many
>>warnings and MD could not be done. I know that its not at all a
>>good idea to increase the 1-4 cut off.
>>
>>
>>The standard advice is to fix the problem with the system, not
>>change the table-extension.
>>
>>
>>By the way to be specific the system size was 12 x 12 x 6 in
>>nm3. I had 256 lipids and about 7300 water molecules.
>>I believe that this might not be the best way to create a
>> larger
>>bilayer system. Could somebody suggest me other ways of doing this?
>>
>>
>>Fix periodicity, then use genconf.
>>
>>-Justin
>>
>>Any help will be appreciated thank you
>>
>>Amit
>>
>>
>>
>>
>>  
>>
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>><mailto:gmx-users@g

Re: [gmx-users] trr file in VMD

[Amit Choubey]

yes you can do that by opening the gro file and then loading the .trr file .

amit

On Sun, Oct 11, 2009 at 6:22 PM, Paymon Pirzadeh wrote:

> Hello,
> How can we use the trr file in VMD? I thought since we ask in the mdp
> file to output the velocities, then in VMD we should be able to see
> molecules colored based on their velocities through the trajectory
> options. Am I correct?
>
> Payman
>
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[gmx-users] question about all atoms lipid molecule structure and force field

[Amit Choubey]

Dear all,
I have been trying to search for an all atom DPPC sructure (including the
missing Hydrogens of long chain hydrocarbons) and then do an all atoms md
simulation on it. I havent yet found any such structure or any force field
that could be used for it on the internet. Is anybody familiar with any such
work ?

Is there any all atom model for hydrocarbons which is incorporated in
Gromacs? I am not 100 % sure about it.

I want to do this to parametrize another force field which essentially uses
all atom model.

Thank you,
Amit
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Re: [gmx-users] question about all atoms lipid molecule structure and force field

[Amit Choubey]

Thank you,
Is it really necessary for me to use Charmm FF for all atom calculations on
lipids?

The reason I am asking this is because it will require me to create gromacs
compatible FF files of the Charmm FF . I did find two perl scripts which can
do probably handle that but i am wondering if the compatible FF are already
up on gromacs website somewhere.


amit


2009/10/14 LuLanyuan 

>  Hi,
> You can find some configurations here:
> http://persweb.wabash.edu/facstaff/fellers/
> And I think you can use Charmm FF.
> Lanyuan
>
> --
> Date: Wed, 14 Oct 2009 11:29:26 -0700
> From: kgp.a...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] question about all atoms lipid molecule structure and
> force field
>
>
> Dear all,
> I have been trying to search for an all atom DPPC sructure (including the
> missing Hydrogens of long chain hydrocarbons) and then do an all atoms md
> simulation on it. I havent yet found any such structure or any force field
> that could be used for it on the internet. Is anybody familiar with any such
> work ?
>
> Is there any all atom model for hydrocarbons which is incorporated in
> Gromacs? I am not 100 % sure about it.
>
> I want to do this to parametrize another force field which essentially uses
> all atom model.
>
> Thank you,
> Amit
>
> --
> Messenger保护盾2.0，更安全可靠的Messenger聊天！ 现在就下载！ 
>
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Re: [gmx-users] question about all atoms lipid molecule

[Amit Choubey]

Hi Par Bjelkmar,

I need to do an all atom simulation for dppc bilayer . You are right the
dppc molecule file that i have has PALM and PCGL residues.

I will like to try to set up the charmm FF for gromacs. But I dont have the
FF files with me, neither do i have the programs. Could you send me a
tutorial or some reference link too ( if you know of any).

Thank you,
Amit







On Thu, Oct 15, 2009 at 4:01 AM, Pär Bjelkmar  wrote:

> Hi,
>
> 15 okt 2009 kl. 07.08 skrev gmx-users-requ...@gromacs.org:
>
>
> The reason I am asking this is because it will require me to create
>
> gromacs compatible FF files of the Charmm FF . I did find two perl
>
> scripts which can do probably handle that but i am wondering if the
>
> compatible FF are already up on gromacs website somewhere.
>
> No, it is not available on the gromacs website yet. You can get the current
> parameter files from me if you'd like to try it out. I'm afraid the DPPC
> lipid in CHARMM is created by combining the PALM and PCGL residues and some
> patches so if you know how that works in CHARMM you might be able to create
> the DPPC residue.
>
>
>
> No one ever said life was easy :)  CHARMM support is under development, you
> can
> get the source via the git repositories, but I don't know its current
> status.
>
> As Justin is saying, CHARMM will be supported as of version 4.1. The source
> code is there in git master branch but you need to get the ff files from
> me.
>
>
>I have been trying to search for an all atom DPPC sructure
>
>(including the missing Hydrogens of long chain hydrocarbons) and
>
>then do an all atoms md simulation on it. I havent yet found any
>
>such structure or any force field that could be used for it on the
>
>internet. Is anybody familiar with any such work ?
>
>
>Is there any all atom model for hydrocarbons which is incorporated
>
>in Gromacs? I am not 100 % sure about it.
>
>
>I want to do this to parametrize another force field which
>
>essentially uses all atom model.
>
>
> /Pär Bjelkmar
>
>
>
> <><><><><><><><><><><><><><><><><><>
>
> Pär Bjelkmar, PhD student
>
>
> Stockholm Center for Biomembrane Research,
>
> Stockholm Bioinformatics Center,
>
> Department of Biochemistry and Biophysics,
>
> Stockholm University
>
>
> Tel:  +46-8-16 2746
>
> Fax: +46-8-15 3679
>
> E-mail: bjelk...@cbr.su.se
>
> Home: http://www.dbb.su.se/User:Bjelkmar
>
> <><><><><><><><><><><><><><><><><><>
>
>
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[gmx-users] gromacs wall parameters

[Amit Choubey]

Hi everyone,
I am trying to model an impenetrable wall for my simulation at z=0. I read
the manual where this thing is discussed. I am still  doubtful about the
options to use.

It seems that the wall parameters are designed to figure out the repulsive
potential function based on wall_type, wall_atomtype, wall_density . So is
it feasible to give any values to the wall parameters except for a really
really low value for wall_density . I am planning to use the wall surface
density for 10-4 potential.

Thank you,
amit
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[gmx-users] Setting up an infinitely hard wall

[Amit Choubey]

Hi everyone,
I have been trying to set up an "infinitely" hard potential wall.

I tried to use the available wall options and could not really get it to do
what i needed. I wanted a steep repulsive potential but when i created that,
the system was blowing up, reason being that it requires smaller time step
and i cant afford to have smaller time step.

My idea to overcome this issue is to just reverse the velocity of the
particle whenever it hits the wall. I am not sure if there is any thing in
GROMACS which does this but any suggestions will be very helpful.

If there is nothing set up for something like above, i would like to play
around with the code to figure it out. If this is the case, could somebody
direct me to a starting point.

Thank you
Amit
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Re: [gmx-users] POPG-Martini Force Field

[Amit Choubey]

On Thu, Oct 22, 2009 at 9:53 AM, S hv  wrote:

>  Hi,
>
> I am currently working with peptide/lipids interactions using the martini
> force field. I want to built a bacterial membrane, so I trying to find the
> topology of the POPG lipid but until now without success.
>


>
> In the martini_v2.0_lipids.itp file, the PG lipids are no included. I have
> seen some works using the martini force field and POPG lipids, e.g., " The
> molecular mechanism monolayer PNAS 105, 10803-10808", but they don't specify
> the topology of POPG lipids.
>

You can do this on your own just pull out the atomic structure of DPPC
and POPG from any website. Compare atomistic DPPC with the Coarse
Grained DPPC and it wont be hard to figure out the POPG CG topology.

BTW, the paper does give a short description about the topology of POPG


> I also tried in the martini web page, but I just found the
> martini_v2.0_lipids.itp file.
>
> Could anyone help me to find such topology?
>
> Thanks a lot for your time,
>
> Salvador
>
> --
> Windows Live: Make it easier for your friends to see what you’re up to on
> Facebook.
>
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[gmx-users] Setting up an infinitely hard wall

[Amit Choubey]

Hi everyone,

I am sending this email again hoping for any quick input for my question.



I have been trying to set up an "infinitely" hard potential wall.

I tried to use the available wall options and could not really get it to do
what i needed. I wanted a steep repulsive potential but when i created that,
the system was blowing up, reason being that it requires smaller time step
and i cant afford to have smaller time step.

My idea to overcome this issue is to just reverse the velocity of the
particle whenever it hits the wall. I am not sure if there is any thing in
GROMACS which does this but any suggestions will be very helpful.

If there is nothing set up for something like above, i would like to play
around with the code to figure it out. If this is the case, could somebody
direct me to a starting point.

Thank you
Amit
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Re: [gmx-users] Setting up an infinitely hard wall

[Amit Choubey]

Hi Berk,
Thank you for the response.

I have obtained distributions with in infinite wall by simulating with an
> softer wall
> and unbiasing with configurations with the wall potential.
>

Could you explain the above ? I am not sure if i get your point.


> But if you need the dynamics, or you want less hassle during the
> simulation,
> you will have to do a bit more effort in coding an infinitely hard wall.
>
> You will not only have to inverse the velocity, but also mirror the
> position
> of the particle in the wall.
>

That's true. I am sorry i didnt mention that.


> This should on require a few lines of code in do_update_md
> in src/mdlib/update.c.
>

Great, I will try this as soon as possible.

>
> Note that this will only work easily when you do not have constraints
> present.
> With constraints things get much more complicated.
>

I do have constraints present. Thank you for pointing this. I am working
with SPC water and I should, in principle be able to figure out the
co-ordinates of all atoms in the molecule if I am given one of the water's
atom's co-ordinate. Does that sound ok?

Thanks for the input again,
Amit


>
> Berk
>
> --
> Date: Thu, 22 Oct 2009 14:34:06 -0700
> From: kgp.a...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Setting up an infinitely hard wall
>
>
> Hi everyone,
>
> I am sending this email again hoping for any quick input for my question.
>
>
>
> I have been trying to set up an "infinitely" hard potential wall.
>
> I tried to use the available wall options and could not really get it to do
> what i needed. I wanted a steep repulsive potential but when i created that,
> the system was blowing up, reason being that it requires smaller time step
> and i cant afford to have smaller time step.
>
> My idea to overcome this issue is to just reverse the velocity of the
> particle whenever it hits the wall. I am not sure if there is any thing in
> GROMACS which does this but any suggestions will be very helpful.
>
> If there is nothing set up for something like above, i would like to play
> around with the code to figure it out. If this is the case, could somebody
> direct me to a starting point.
>
>  Thank you
> Amit
>
>
> --
> New Windows 7: Find the right PC for you. Learn 
> more.
>
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Re: [gmx-users] POPG-Martini Force Field

[Amit Choubey]

On Fri, Oct 23, 2009 at 12:33 AM, XAvier Periole  wrote:

>
> On Oct 22, 2009, at 11:28 PM, Amit Choubey wrote:
>
>
>
> On Thu, Oct 22, 2009 at 9:53 AM, S hv  wrote:
>
>>  Hi,
>>
>> I am currently working with peptide/lipids interactions using the martini
>> force field. I want to built a bacterial membrane, so I trying to find the
>> topology of the POPG lipid but until now without success.
>>
>
>
>>
>> In the martini_v2.0_lipids.itp file, the PG lipids are no included. I have
>> seen some works using the martini force field and POPG lipids, e.g., " The
>> molecular mechanism monolayer PNAS 105, 10803-10808", but they don't specify
>> the topology of POPG lipids.
>>
>
>
> You can do this on your own just pull out the atomic structure of DPPC and 
> POPG from any website. Compare atomistic DPPC with the Coarse Grained DPPC 
> and it wont be hard to figure out the POPG CG topology.
>
> That is certainly not that easy. A lot of parameterizations efforts have to
> be
> involved.
>

No, thats easy because you are working with a coarse grained model. There
are are only few types of particles possible. The only tricky ones are the
head groups which the paper does mention.

>
>
> BTW, the paper does give a short description about the topology of POPG
>
> The best is probably to ask the authors of that paper to share their
> topology,
> which they should.
>
>
>
>> I also tried in the martini web page, but I just found the
>> martini_v2.0_lipids.itp file.
>>
>> Could anyone help me to find such topology?
>>
>> Thanks a lot for your time,
>>
>> Salvador
>>
>> --
>> Windows Live: Make it easier for your friends to see what you’re up to on
>> Facebook.<http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009>
>>
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Re: [gmx-users] Setting up an infinitely hard wall

[Amit Choubey]

Hi Berk,

I am mailing about the issue of setting up infinite potential well.

I now want to simplify the task of inversing the velocity and mirroring the
particle by the following procedure. If a particle is found in z wrote:

>  Hi,
>
> If you have a wall potential, you can reweight the configurations
> with weight 0 if one or more particles are beyond the wall
> and exp(Vwall/kT) if no particles are beyond the wall.
> This will only work efficiently if you choose the wall potential in a smart
> way.
> I managed to get an efficiency of 70%.
>
> If you have constraints, an atom that goes beyond the wall is directly
> coupled to the atoms it is constrained to. You will have to work out
> the equations for such a situation. It might be as simple that you can
> just correct x and v for the atom that went beyond the wall and then
> apply the constraints as normal.
>
> Berk
>
> --
> Date: Fri, 23 Oct 2009 00:26:08 -0700
> Subject: Re: [gmx-users] Setting up an infinitely hard wall
>
> From: kgp.a...@gmail.com
> To: gmx-users@gromacs.org
>
> Hi Berk,
>
> Thank you for the response.
>
> I have obtained distributions with in infinite wall by simulating with an
> softer wall
> and unbiasing with configurations with the wall potential.
>
>
> Could you explain the above ? I am not sure if i get your point.
>
>
> But if you need the dynamics, or you want less hassle during the
> simulation,
> you will have to do a bit more effort in coding an infinitely hard wall.
>
> You will not only have to inverse the velocity, but also mirror the
> position
> of the particle in the wall.
>
>
> That's true. I am sorry i didnt mention that.
>
>
> This should on require a few lines of code in do_update_md
> in src/mdlib/update.c.
>
>
> Great, I will try this as soon as possible.
>
>
> Note that this will only work easily when you do not have constraints
> present.
> With constraints things get much more complicated.
>
>
> I do have constraints present. Thank you for pointing this. I am working
> with SPC water and I should, in principle be able to figure out the
> co-ordinates of all atoms in the molecule if I am given one of the water's
> atom's co-ordinate. Does that sound ok?
>
> Thanks for the input again,
> Amit
>
>
>
> Berk
>
> --
> Date: Thu, 22 Oct 2009 14:34:06 -0700
> From: kgp.a...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Setting up an infinitely hard wall
>
>
> Hi everyone,
>
> I am sending this email again hoping for any quick input for my question.
>
>
>
> I have been trying to set up an "infinitely" hard potential wall.
>
> I tried to use the available wall options and could not really get it to do
> what i needed. I wanted a steep repulsive potential but when i created that,
> the system was blowing up, reason being that it requires smaller time step
> and i cant afford to have smaller time step.
>
> My idea to overcome this issue is to just reverse the velocity of the
> particle whenever it hits the wall. I am not sure if there is any thing in
> GROMACS which does this but any suggestions will be very helpful.
>
> If there is nothing set up for something like above, i would like to play
> around with the code to figure it out. If this is the case, could somebody
> direct me to a starting point.
>
>  Thank you
> Amit
>
>
> --
> New Windows 7: Find the right PC for you. Learn 
> more.
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] calculating local pressure

[Amit Choubey]

Hi Everyone,


I have been looking at ways to calculate local pressure for a simulation. I
found a gromacs package called
gromacs-localp-3.0.2.tgz
  at the following page

http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Gromacs_binaries

I was wondering if you know about a more recent package which implements the
calculation of local pressure. I actually need the virial for each atom, so
do you have any idea if this package writes these somewhere.

A man page on the local pressure calculation would be wonderful.

Thank you,
Amit
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[gmx-users] Re: Walls In Gromacs

[Amit Choubey]

On Tue, Nov 10, 2009 at 4:32 AM, Marcovitz Amir wrote:

> Hi Amit,
>
> Unfortunately, i don't have an answer to your question as i am a very
> new GROMACS user myself..
> Actually i might need your help.
>


> I need to model two charged plates with opposite signs which are
> solvated in an electrolyte solution.


You might try to start with a boundary condition on the potential say
something like constant potential on the plates. And then you can always
find the electrostatic Green's function that solves the poisson's equation.
>From there you could derive an expression for the potential in the box if
the charge density were provided. This part is discussed in Classic
Electrodynamics book by Jackson. Have a look at it if you need reference.

You can use the above green's function for finding potential everywhere in
box depending on the location of ions in the solution. The force due to this
can then be implemented in MD. I am not very sure about the implementation
though.


> When I was desperately browsing for
> keywords such as: Gromacs plates, walls, etc., trying to find the
> slightest clue of how to approach this issue in gromacs i saw your
> posting from the October 19th.
>
> I will most appreciate if you can give me some hint or tip of how to
> approach this problem or what is the suitable chapter in the manual to
> search for it.
>

I am not sure about any discussion on the specific type of things you are
talking about. Wall function for MD simulation is disscussed in chapter 7.
You will only find what options can be used. I think a tabulated function
can also be used.


> Sorry i couldn't help you with your question, hopefully you already
> figured it out,
>


I think it beneficial for both of us to keep these discussion in the forum
for our and other's benefit .

Amit

>
> Regards,
> Amir Marcovitz,
> Weizmann Inst. of Science , Rehovot, Israel
>
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[gmx-users] doing exact continuation

[Amit Choubey]

Hi everyone,

I want to do an exact continuation with saved configuration and velocity.
What are the options that i need to change in mdp file?

I know i have to make unconstrained_start = yes. Anything else?

The reason i am asking this is that it is kind of difficult to make sure if
i am doing the right thing by comparing two different trajectories. This is
because the trajectories are generally 'chaotic' and they diverge even if
there is a difference in the numbers due to the machine. So i want to do the
best from my part.

thank you,
Amit
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Re: [gmx-users] How to generate xvg files

[Amit Choubey]

On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz 
wrote:

> Hi I am trying to generate xvg files for my simulation. Which
> parameter do I need to specify?
>

xvg files for what? They are used for data files for 2D plots of quantities
that can be analyzed...

Can you be more specific?

amit

>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
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Re: [gmx-users] How to generate xvg files

[Amit Choubey]

On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz 
wrote:

> Actually I guess I need to generate the xtc first before I can get the xvg
>
> I am trying to develop a workflow for this
> mdrun
> g dist calculates the distances between the centers of mass of two groups
> g bond calculates distances between atoms
> g msd calculates mean square displacements
> g rms calculates rmsd’s with a reference structure and rmsd matrices
> g rmsf calculates atomic fluctuations
> g energy writes energies to xvg files and displays averages
>

Thats true. First you need to do the simulation 'mdrun' and then analyze the
trajectory (.xtc) and energy (.edr) files generated. It takes quite some
time to figure out the first step 'mdrun' :)

amit




>
> On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey  wrote:
> >
> >
> > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz  >
> > wrote:
> >>
> >> Hi I am trying to generate xvg files for my simulation. Which
> >> parameter do I need to specify?
> >
> > xvg files for what? They are used for data files for 2D plots of
> quantities
> > that can be analyzed...
> > Can you be more specific?
> > amit
> >>
> >> --
> >> Jack
> >>
> >> http://drugdiscoveryathome.com
> >> http://hydrogenathome.org
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at http://www.gromacs.org/search before
> posting!
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> >
> >
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>
>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
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Re: [gmx-users] How to generate xvg files

[Amit Choubey]

On Tue, Nov 10, 2009 at 7:02 PM, Jack Shultz 
wrote:

> I'm trying to get the xtc output. The mdp file has these parameters.
> Is the nstxtcout what specifiies it to generate xtc?
>
yes its the freq of writing co - ordinates

> nsteps  = 2000  ; Maximum number of (minimization)
> steps to perform
> nstenergy   = 10; Write energies to disk every nstenergy
> steps
> nstxtcout   = 10; Write coordinates to disk every
> nstxtcout steps
>
> Do I need to use this -x flag?
> mdrun -nice 0 -s em.tpr -x
> No xtc was created though
>
-x is for writing xtc file
http://manual.gromacs.org/current/online/mdrun.html should help

>
> On Tue, Nov 10, 2009 at 9:43 PM, Amit Choubey  wrote:
> >
> >
> > On Tue, Nov 10, 2009 at 6:31 PM, Jack Shultz  >
> > wrote:
> >>
> >> Actually I guess I need to generate the xtc first before I can get the
> xvg
> >>
> >> I am trying to develop a workflow for this
> >> mdrun
> >> g dist calculates the distances between the centers of mass of two
> groups
> >> g bond calculates distances between atoms
> >> g msd calculates mean square displacements
> >> g rms calculates rmsd’s with a reference structure and rmsd matrices
> >> g rmsf calculates atomic fluctuations
> >> g energy writes energies to xvg files and displays averages
> >
> > Thats true. First you need to do the simulation 'mdrun' and then analyze
> the
> > trajectory (.xtc) and energy (.edr) files generated. It takes quite some
> > time to figure out the first step 'mdrun' :)
> > amit
> >
> >
> >>
> >> On Tue, Nov 10, 2009 at 9:24 PM, Amit Choubey 
> wrote:
> >> >
> >> >
> >> > On Tue, Nov 10, 2009 at 6:11 PM, Jack Shultz
> >> > 
> >> > wrote:
> >> >>
> >> >> Hi I am trying to generate xvg files for my simulation. Which
> >> >> parameter do I need to specify?
> >> >
> >> > xvg files for what? They are used for data files for 2D plots of
> >> > quantities
> >> > that can be analyzed...
> >> > Can you be more specific?
> >> > amit
> >> >>
> >> >> --
> >> >> Jack
> >> >>
> >> >> http://drugdiscoveryathome.com
> >> >> http://hydrogenathome.org
> >> >> --
> >> >> gmx-users mailing listgmx-users@gromacs.org
> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> >> Please search the archive at http://www.gromacs.org/search before
> >> >> posting!
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> >> >> www interface or send it to gmx-users-requ...@gromacs.org.
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> >> >
> >> >
> >> > --
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> >> >
> >>
> >>
> >>
> >> --
> >> Jack
> >>
> >> http://drugdiscoveryathome.com
> >> http://hydrogenathome.org
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >
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>
>
> --
> Jack
>
> http://drugdiscoveryathome.com
> http://hydrogenathome.org
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>
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Re: [gmx-users] Can not open file; traj.trr

[Amit Choubey]

in your previous run you might be saving the trajectory in some other *.trr
file . Try appending in that.

amit

On Fri, Nov 13, 2009 at 9:11 AM, Yi Peng  wrote:

> Hi, everyone,
>
> I was using Gromacs-4.0.3 to run my MD calculations parallell on our High
> performance clusters for a large system which was crashed because I run out
> the time limits. So I tried to resume my calculations by the script as
> follows:
>
> #PBS -N gromacs
> #PBS -l walltime=250:00:00
> #PBS -l nodes=8:ppn=2:quad
> #PBS -j oe
> echo Using nodes
> cat $PBS_NODEFILE
> module load mpich
> module load intel-f
> module load gromacs-4.0.3
> cd $PBS_O_WORKDIR
> cd /home/yxp17/impd/impd1/wt_wo
> /usr/local/bin/mpiexec mdrun -multi 16 -s md.tpr -cpi state.cpt -append
>
>
> But it will stop and show the message as follows
>
> "Whatever Happened to Pong ?" (F. Black)
> Halting program mdrun
> gcq#180: "Whatever Happened to Pong ?" (F. Black)
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
> p0_12952:  p4_error: : -1
> p4_error: latest msg from perror: No such file or directory
> ---
> Program mdrun, VERSION 4.0.3
> Source code file: gmxfio.c, line: 736
> Can not open file:
> traj.trr
> ---
> How can I solve the problem? Thanks a lot
>
> Yi
>
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Re: [gmx-users] Segmentation fault while running MD simulation

[Amit Choubey]

hi,

could you specify the system size?

How many steps did it run before you got the segmentation fault? Try to find
if everything went ok until the segmentation fault by saving log and
trajectories.

amit



On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul  wrote:

>
>
> rainy...@yahoo.com wrote:
>
>> Hi,
>>
>> The relevant lines of my script are the following:
>>
>> line 27: # Run MD and write output to /nas2 disk
>> line 28: $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c
>> confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr
>> line 29:
>> line 30: # MDRUN completes: now make the next run file for a further 200
>> ps, to be run by next job
>> line 31: $TPBCONV -s npg3_4.tpr -f npg3_4.trr -e npg3_4.edr -o
>> npg3_4_2.tpr -extend 20
>>
>>
>> Since line 31 would be carried out after line 28, I'm not sure why the
>> comment "-s: command not found" is relevant?
>>
>>
> Because mdrun is exiting, so the script is moving on.  Perhaps the system
> isn't recognizing the $TPBCONV environment variable, and thus is
> interpreting "-s" as a separately command rather than an option passed to
> tpbconv.
>
> -Justin
>
>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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] Handling modified residue

[Amit Choubey]

you could try to write your top files in the working directory and use
pdb2gmx -ff option. By default, gromacs first searches in the working
directory.

amit

On Sat, Nov 14, 2009 at 9:05 AM, Jiang Zhu  wrote:

> Dear all,
>
> I have been a GROMACS user for some time but this is my first time
> to handle a modified residue with an additional chemical group linked to the
> side chain. I do not have the permission to change/add the topology file in
> the system directory where GROMACS package is located. I am wondering if
> there is any other way to force pdbgmx to read residue topo file from
> specified location or other tricks I can play. Thanks for your help!
>
> Best regards,
> Jiang
>
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Re: [gmx-users] Problem with box-type after the extension of simulation

[Amit Choubey]

On Wed, Nov 18, 2009 at 9:29 PM, sukesh chandra gain wrote:

> Dear All,
> I started a protein simulation for 100ps with octahedron box. After
> completion of that run I visualized the protein at the centre of the
> octahedron box by using trjconv.
> Then I have extended the simulation for another 500 ps by using tpbconv.
> But now it is showing as cubic box when I see the result after using
> trajconv (additionally some part of the protein is out of the box).


This could only be a visualization glitch.
Try using trjconv options.

amit


> I do not have any clue how the box type has been changed or where could I
> go wrong.
> Please comment.
> Thank you,
> Cheers,
> Sukesh
>
> --
> Sukesh Chandra Gain
> TCS Innovation Labs
> Tata Consultancy Services Ltd.
> 'Deccan Park', Madhapur
> Hyderabad 500081
> Phone:  +91 40 6667 3572
>
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[gmx-users] g_angle for calculating dihedrals

[Amit Choubey]

Hi everyone,

I was looking at calculation od dihedrals using g_angle. I did not
understand what the output of this tool is, along the x-axis we have angle
(in degrees) but what do we have along the y axis . Does y-axis show the
fraction of dihedrals having that specific angle? It does seem so by adding
all the fractions but i need to make sure.

Just to be sure that you know what i am talking about i first used make_ndx
to make a group of 4 atoms (whose dihedral has to be calculated) . Then i
used

g_angle -f confout.gro -n index.ndx -type dihedral

where index.ndx has the indices for all the relevant atoms stored in a
group.

Thank you,

Amit
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[gmx-users] doing averages using g_angle

[Amit Choubey]

Hi everyone,

I am trying to analyze dihedrals of molecules after a simulation. I am able
to calculate dihedral distribution at ant particular time using g
-angle and proper group using

g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od dihed12

This gives me the distribution at t=800 ps . What i really want is to see
the dihedral distribution at all time steps (after 800 ps) in one go, and
may be do some averaging later. Is there a straight forward way to do this.
I can imagine that i could write a script file that could do this but then i
dont want to deal with a lot of files, i rather want everything to be saved
in a single file with multiple columns. Could someone suggest a trick for
this?

Thank you,
Amit
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Re: [gmx-users] doing averages using g_angle

[Amit Choubey]

Hi Mark,

It does seem that the -all option averages the distributions.
The thing is i was confused with "the first graph is the average, the rest
are the individual angles." because when i tried it previously i only found
2 columns which were angle and distribution.

But now i checked again explicitly by doing few more g_angle commands and it
seems that -all does do what i wanted to do. I still dont know what the
"rest are the individual angles" means.



Thank you,
Amit






On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham wrote:

> Amit Choubey wrote:
>
>> Hi everyone,
>>
>> I am trying to analyze dihedrals of molecules after a simulation. I am
>> able to calculate dihedral distribution at ant particular time using g
>> -angle and proper group using
>>
>> g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od dihed12
>>
>> This gives me the distribution at t=800 ps . What i really want is to see
>> the dihedral distribution at all time steps (after 800 ps) in one go, and
>> may be do some averaging later. Is there a straight forward way to do this.
>> I can imagine that i could write a script file that could do this but then i
>> dont want to deal with a lot of files, i rather want everything to be saved
>> in a single file with multiple columns. Could someone suggest a trick for
>> this?
>>
>
> The first paragraph of g_angle -h suggests there's an option where "the
> first graph is the average, the rest are the individual angles." Does this
> work?
>
>
> Mark
> --
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Re: [gmx-users] doing averages using g_angle

[Amit Choubey]

Hi Mark,

Ok here is the command line i used :-

g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all

output is

# This file was created Tue Dec  1 20:20:41 2009
# by the following command:
# g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
#
# g_angle is part of G R O M A C S:
#
# Go Rough, Oppose Many Angry Chinese Serial killers
#
@title "Dihedral Distribution: C34_C36_C37_C38"
@xaxis  label "Degrees"
@yaxis  label ""
@TYPE xy
@subtitle "average angle: 9.87432\So\N"
@with g0
@world xmin -180
@world xmax  180
@world ymin 0
@world ymax 0.0451172
@xaxis  tick major 60
@xaxis  tick minor 30
@yaxis  tick major 0.005
@yaxis  tick minor 0.0025
  -1800.015625
  -1790.011719
  -1780.015625
  -1770.00
  -1760.035156
  -1750.031250
  -1740.019531
  -1730.019531
  -1720.023438
  -1710.015625
  -1700.015625

I did not include the distribution for rest of the angles.

The second column is the fractional distribution of dihedrals with the
corresponding angle in the 1st column.

The distribution is averaged over time t = 800ps and 802 ps snapshots. I
checked this part.

Amit




On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham wrote:

> Amit Choubey wrote:
>
>> Hi Mark,
>>
>> It does seem that the -all option averages the distributions. The thing is
>> i was confused with "the first graph is the average, the rest are the
>> individual angles." because when i tried it previously i only found 2
>> columns which were angle and distribution.
>>
>> But now i checked again explicitly by doing few more g_angle commands and
>> it seems that -all does do what i wanted to do. I still dont know what the
>> "rest are the individual angles" means.
>>
>
> I haven't ever used it, but would have expected the output to be along the
> lines of
>
> Time "Average over all angles" Angle-1 Angle-2 ...
> 1  234   23  345
> 2  123   234 232
> 2  223   ...
> 3      323
>
> What output do you get and what seems wrong to you?
>
> Mark
>
>  On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham > mark.abra...@anu.edu.au>> wrote:
>>
>>Amit Choubey wrote:
>>
>>Hi everyone,
>>
>>I am trying to analyze dihedrals of molecules after a
>>simulation. I am able to calculate dihedral distribution at ant
>>particular time using g
>>-angle and proper group using
>>
>>g_angle -f after_md.trr -b 800 -type dihedral -n chain1.ndx -od
>>dihed12
>>
>>This gives me the distribution at t=800 ps . What i really want
>>is to see the dihedral distribution at all time steps (after 800
>>ps) in one go, and may be do some averaging later. Is there a
>>straight forward way to do this. I can imagine that i could
>>write a script file that could do this but then i dont want to
>>deal with a lot of files, i rather want everything to be saved
>>in a single file with multiple columns. Could someone suggest a
>>trick for this?
>>
>>
>>The first paragraph of g_angle -h suggests there's an option where
>>"the first graph is the average, the rest are the individual
>>angles." Does this work?
>>
>>
>>Mark
>>--gmx-users mailing listgmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/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
>><mailto:gmx-users-requ...@gromacs.org>.
>>
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>>
>>
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Re: [gmx-users] doing averages using g_angle

[Amit Choubey]

Hi Mark,

That is true. But what does the manual refer to when it says

the first graph is the average, the rest are the individual angles

what and where are the rest? I am only curious because there might be a
hidden feature that could be useful for me.

Amit

On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham wrote:

> Amit Choubey wrote:
>
>> Hi Mark,
>>
>> Ok here is the command line i used :-
>>
>> g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
>> output is
>> # This file was created Tue Dec  1 20:20:41 2009
>> # by the following command:
>> # g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e 804 -all
>> #
>> # g_angle is part of G R O M A C S:
>> #
>> # Go Rough, Oppose Many Angry Chinese Serial killers
>> #
>> @title "Dihedral Distribution: C34_C36_C37_C38"
>>
>
> This title makes it look like there is only one angle in your index file.
>
> Mark
>
>  @xaxis  label "Degrees"
>> @yaxis  label ""
>> @TYPE xy
>> @subtitle "average angle: 9.87432\So\N"
>> @with g0
>> @world xmin -180
>> @world xmax  180
>> @world ymin 0
>> @world ymax 0.0451172
>> @xaxis  tick major 60
>> @xaxis  tick minor 30
>> @yaxis  tick major 0.005
>> @yaxis  tick minor 0.0025
>>  -1800.015625
>>  -1790.011719
>>  -1780.015625
>>  -1770.00
>>  -1760.035156
>>  -1750.031250
>>  -1740.019531
>>  -1730.019531
>>  -1720.023438
>>  -1710.015625
>>  -1700.015625
>>
>> I did not include the distribution for rest of the angles.
>>  The second column is the fractional distribution of dihedrals with the
>> corresponding angle in the 1st column.
>>
>> The distribution is averaged over time t = 800ps and 802 ps snapshots. I
>> checked this part.
>>
>> Amit
>>
>>
>>
>>
>> On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham > mark.abra...@anu.edu.au>> wrote:
>>
>>Amit Choubey wrote:
>>
>>Hi Mark,
>>
>>It does seem that the -all option averages the distributions.
>>The thing is i was confused with "the first graph is the
>>average, the rest are the individual angles." because when i
>>tried it previously i only found 2 columns which were angle and
>>distribution.
>>
>>But now i checked again explicitly by doing few more g_angle
>>commands and it seems that -all does do what i wanted to do. I
>>still dont know what the "rest are the individual angles" means.
>>
>>
>>I haven't ever used it, but would have expected the output to be
>>along the lines of
>>
>>Time "Average over all angles" Angle-1 Angle-2 ...
>>1  234   23  345
>>2  123   234 232
>>2  223   ...
>>3  323
>>
>>What output do you get and what seems wrong to you?
>>
>>Mark
>>
>>On Tue, Dec 1, 2009 at 6:52 PM, Mark Abraham
>>mailto:mark.abra...@anu.edu.au>
>><mailto:mark.abra...@anu.edu.au
>><mailto:mark.abra...@anu.edu.au>>> wrote:
>>
>>   Amit Choubey wrote:
>>
>>   Hi everyone,
>>
>>   I am trying to analyze dihedrals of molecules after a
>>   simulation. I am able to calculate dihedral distribution
>>at ant
>>   particular time using g
>>   -angle and proper group using
>>
>>   g_angle -f after_md.trr -b 800 -type dihedral -n
>>chain1.ndx -od
>>   dihed12
>>
>>   This gives me the distribution at t=800 ps . What i
>>really want
>>   is to see the dihedral distribution at all time steps
>>(after 800
>>   ps) in one go, and may be do some averaging later. Is there
>> a
>>   straight forward way to do this. I can imagine that i could
>>   write a script file that could do this but then i dont
>>want to
>>   deal with a lot of files, i rather want everything to be
>>saved
>>   in a single file with multiple columns. Could someone
>>suggest a
>>   trick fo

Re: [gmx-users] doing averages using g_angle

[Amit Choubey]

On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi Mark,
>>
>> That is true. But what does the manual refer to when it says
>> the first graph is the average, the rest are the individual angles
>>
>> what and where are the rest? I am only curious because there might be a
>> hidden feature that could be useful for me.
>>
>>
> Read all of the help information; the command in the .xvg file below shows
> that you're not yet using the right output options.  Hint: look at the
> sentence in g_angle -h before the one quoted above, as well as the -ov
> flag...
>

-ov flag gives the average value of angle of the group with time. This is
not very useful for me right now.

I am interested in the distribution of dihedrals with angle.

I was just curious about the -all features...



>
> -Justin
>
>  Amit
>>
>>
>> On Wed, Dec 2, 2009 at 12:21 AM, Mark Abraham 
>> > mark.abra...@anu.edu.au>> wrote:
>>
>>Amit Choubey wrote:
>>
>>Hi Mark,
>>
>>Ok here is the command line i used :-
>>
>>g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e
>>804 -all
>>output is
>># This file was created Tue Dec  1 20:20:41 2009
>># by the following command:
>># g_angle -f after_md.trr -type dihedral -n chain1.ndx -b 800 -e
>>804 -all
>>#
>># g_angle is part of G R O M A C S:
>>#
>># Go Rough, Oppose Many Angry Chinese Serial killers
>>#
>>@title "Dihedral Distribution: C34_C36_C37_C38"
>>
>>
>>This title makes it look like there is only one angle in your index
>>file.
>>
>>Mark
>>
>>@xaxis  label "Degrees"
>>@yaxis  label ""
>>@TYPE xy
>>@subtitle "average angle: 9.87432\So\N"
>>@with g0
>>@world xmin -180
>>@world xmax  180
>>@world ymin 0
>>@world ymax 0.0451172
>>@xaxis  tick major 60
>>@xaxis  tick minor 30
>>@yaxis  tick major 0.005
>>@yaxis  tick minor 0.0025
>> -1800.015625
>> -1790.011719
>> -1780.015625
>> -1770.00
>> -1760.035156
>> -1750.031250
>> -1740.019531
>> -1730.019531
>> -1720.023438
>> -1710.015625
>> -1700.015625
>>
>>I did not include the distribution for rest of the angles.
>> The second column is the fractional distribution of dihedrals
>>with the corresponding angle in the 1st column.
>>
>>The distribution is averaged over time t = 800ps and 802 ps
>>snapshots. I checked this part.
>>
>>Amit
>>
>>
>>
>>
>>On Tue, Dec 1, 2009 at 8:15 PM, Mark Abraham
>>mailto:mark.abra...@anu.edu.au>
>><mailto:mark.abra...@anu.edu.au
>><mailto:mark.abra...@anu.edu.au>>> wrote:
>>
>>   Amit Choubey wrote:
>>
>>   Hi Mark,
>>
>>   It does seem that the -all option averages the
>> distributions.
>>   The thing is i was confused with "the first graph is the
>>   average, the rest are the individual angles." because when i
>>   tried it previously i only found 2 columns which were
>>angle and
>>   distribution.
>>
>>   But now i checked again explicitly by doing few more g_angle
>>   commands and it seems that -all does do what i wanted to
>>do. I
>>   still dont know what the "rest are the individual angles"
>>means.
>>
>>
>>   I haven't ever used it, but would have expected the output to be
>>   along the lines of
>>
>>   Time "Average over all angles" Angle-1 Angle-2 ...
>>   1  234   23  345
>>   2  123   234 232
>>   2  223   ...
>>   3  323
>>
>>   What output do you get and what seems wrong to you?
>>
>>   Mark
>>
>>

Re: [gmx-users] doing averages using g_angle

[Amit Choubey]

Hi Justin,

Yes I understand what you are saying.

Thank you

amit

On Wed, Dec 2, 2009 at 12:50 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>
>>
>> On Wed, Dec 2, 2009 at 12:07 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>Hi Mark,
>>
>>That is true. But what does the manual refer to when it says
>>the first graph is the average, the rest are the individual angles
>>
>>what and where are the rest? I am only curious because there
>>might be a hidden feature that could be useful for me.
>>
>>
>>Read all of the help information; the command in the .xvg file below
>>shows that you're not yet using the right output options.  Hint:
>>look at the sentence in g_angle -h before the one quoted above, as
>>well as the -ov flag...
>>
>>
>> -ov flag gives the average value of angle of the group with time. This is
>> not very useful for me right now.
>>
>
> By using -ov -all, the first column is the average of all groups analyzed,
> and probably is not useful for your purpose, but the subsequent columns are
> the value of the chosen angles at each time frame.  From these data, you
> could pretty easily write a script that calculates the distributions by
> binning.
>
> -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/search before posting!
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Re: [gmx-users] box size & continuing the previous energy minimization

[Amit Choubey]

On Thu, Dec 23, 2010 at 2:41 PM, mustafa bilsel  wrote:

> Hi,
>
> 1. How can I learn the box shape and size of a completed simulation?
>

check the end of the resulting gro file .


> 2. I want to keep going the previous completed energy minimization by
> increasing nsteps. How can I do this?
>

increase in nsteps, and may be the tolerance too.


>
> Best wishes
> Mustafa
>
>
> --
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Re: [gmx-users] Signal: Segmentation faul

[Amit Choubey]

Your log file does indicate that the steepest descent converged. I dont know
why you have the error messages. Why not go ahead with MD ?

Amit

On Sun, Jan 2, 2011 at 10:35 PM, shikha agarwal wrote:

> hi,
> HAPPY NEW YEAR
>
> I am experiencing a segmentation fault during mdrun in equlibration step .
> error
>
> Wrote pdb files with previous and current coordinates
> [shikha-desktop:01719] *** Process received signal ***
> [shikha-desktop:01719] Signal: Segmentation fault (11)
> [shikha-desktop:01719] Signal code: Address not mapped (1)
> [shikha-desktop:01719] Failing at address: 0x8d22a70
> [shikha-desktop:01719] [ 0] [0xb87410]
> [shikha-desktop:01719] [ 1] mdrun(do_nonbonded+0x769) [0x82a9789]
> [shikha-desktop:01719] *** End of error message ***
> Segmentation fault
>
>
>
>
>
> bottom lines of my .log file after energy minimization is this
>
>
>
>  Step   Time Lambda
>   1135711357.00.0
>
>Step   Time Lambda
>   1135811358.00.0
>
>Step   Time Lambda
>   1135911359.00.0
>
>Step   Time Lambda
>   1136011360.00.0
>
>Step   Time Lambda
>   1136111361.00.0
>
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
>
> Steepest Descents converged to machine precision in 11362 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -5.4871900e+06
> Maximum force =  3.9830833e+03 on atom 4511
> Norm of force =  1.9521437e+01
>
> M E G A - F L O P S   A C C O U N T I N G
>
>RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
>T=TabulatedW3=SPC/TIP3pW4=TIP4p (single or pairs)
>NF=No Forces
>
>  Computing:   M-Number M-Flops  % Flops
>
> -
>  LJ   10523.695513  347281.952 0.4
>  Coul(T)   6405.625131  269036.256 0.3
>  Coul(T) [W3]   226.446553   28305.819 0.0
>  Coul(T) + LJ  4637.739866  255075.693 0.3
>  Coul(T) + LJ [W3] 1706.661036  235519.223 0.3
>  Coul(T) + LJ [W3-W3]141595.84421154089612.48969.1
>  Outer nonbonded loop 18947.604080  189476.041 0.2
>  1,4 nonbonded interactions 105.1893969467.046 0.0
>  Calc Weights 11755.000218  423180.008 0.5
>  Spread Q Bspline250773.337984  501546.676 0.6
>  Gather F Bspline250773.337984 1504640.028 1.9
>  3D-FFT 1217431.505524 9739452.04412.4
>  Solve PME14842.953216  949949.006 1.2
>  NS-Pairs418574.562328 8790065.80911.2
>  Reset In Box  1338.8867184016.660 0.0
>  Shift-X   3916.765450   23500.593 0.0
>  CG-CoM3918.333406   11755.000 0.0
>  Bonds  114.1312906733.746 0.0
>  Angles 142.695358   23972.820 0.0
>  Propers102.167104   23396.267 0.0
>  Impropers   28.9844626028.768 0.0
>  RB-Dihedrals 2.885948 712.829 0.0
>  Pos. Restr. 38.1990441909.952 0.0
>  Virial3918.844696   70539.205 0.1
>  Settle2534.725856  818716.451 1.0
>
> -
>  Total78323890.379   100.0
>
> -
>
>
>  R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>
>  Computing: Nodes Number G-CyclesSeconds %
> ---
>  Neighbor search1  1136230337.457 6067.718.8
>  Force  1  1136235859.263 7172.122.3
>  PME mesh   1  1136212486.060 2497.3 7.8
>  Constraints1  22723 1294.000  258.8 0.8
>  Rest   1   81096.73016219.8

Re: [gmx-users] so difficult problem

[Amit Choubey]

There is something wrong with your initial configuration. May be you forgot
to take care of periodicity, how did you get your initial configuration?
Also notice that these kind of problems have been discussed previously.

Amit

On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Dear All
> I am using this .mdp file and I recived the below warnings,I can't solve
> that.
>
>
> title= NPT
> define   =
> integrator   = md
> tinit= 0
> dt   = 0.002
> nsteps   = 50
> nstcomm  = 1
> comm-grps= protein non-protein
> niter= 20
> nstxout  = 5000
> nstvout  = 5000
> nstfout  = 0
> nstlog   = 5000
> nstenergy= 250
> nstxtcout= 250
> xtc-precision= 1000
> xtc_grps = protein non-protein
> energygrps   = Protein  non-protein
> nstlist  = 5
> ns_type  = grid
> pbc  = xyz
> rlist= 1.4
> domain-decomposition = no
> coulombtype  = PME
> rcoulomb-switch  = 0
> rcoulomb = 1.4
> epsilon-r= 1
> vdw-type = Cut-off
> rvdw-switch  = 0
> rvdw = 1.4
> DispCorr = EnerPres
> fourierspacing   = 0.12
> fourier_nx   = 0
> fourier_ny   = 0
> fourier_nz   = 0
> pme_order= 4
> ewald_rtol   = 1e-05
> epsilon_surface  = 0
> optimize_fft = no
> tcoupl   = Nose-hoover
> tc-grps  = Protein non-protein
> tau_t= 0.1  0.1
> ref_t= 300  300
> Pcoupl   = Parrinello-Rahman
> Pcoupltype   = Isotropic
> tau_p= 1.0
> compressibility  = 4.5e-5
> ref_p= 1.0
> annealing= no
> gen_vel  = yes
> gen_temp = 310
> gen_seed = 173529
> constraints  = all-bonds
> constraint-algorithm = Lincs
> unconstrained-start  = no
> lincs-order  = 4
> lincs-warnangle  = 30
> morse= no
>
> my sytem is protein-ligand,I want to generate a NPT.
> the result was:
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
> starting mdrun 'Protein in water'
> 50 steps,   1000.0 ps.
>
> Step 0, time 0 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>5264   5263   41.70.1143   0.1261  0.1140
>5293   5294   82.70.1221 2612.9744  0.1090
>5291   5293   77.20.1517 6082.6147  0.1390
>5291   5292  101.00.1117 1518.6106  0.1090
>5289   5291   87.70.1353 6891.8911  0.1390
>5289   5290   88.40.1437 7529.4878  0.1360
>5289   5287   88.40.1456 7540.4873  0.1390
>5287   5288   89.70.1092 381.5114  0.1090
>5285   5287   92.30.1395 354.9220  0.1390
>5285   5286  123.80.1101  44.8448  0.1090
>5284   5293   89.00.1478 4605.1763  0.1390
>5284   5285   79.30.1402 173.5627  0.1390
>5278   5279   78.90.1529   1.1270  0.1530
>5277   5278  122.90.1545  13.1423  0.1530
>5276   5284   84.90.1422 159.0098  0.1390
>5276   5277   68.40.1543  90.8248  0.1530
>5276   5275   39.50.1439  72.5216  0.1430
>5274   5275  103.70.1436  21.6028  0.1430
>5273   5274  108.50.1394   3.3421  0.1390
>5276   5272   45.70.1402  80.6795  0.1390
>5272   5273  127.30.1340  14.2401  0.1330
>5272   5270   69.80.1336  12.6250  0.1330
>5270   5271  113.30.1092   0.2530  0.1090
>5268   5270  104.60.1391   0.2718  0.1390
>5268   5269   44.40.1091   0.1636  0.1090
>5273   5266   58.50.1342  14.0125  0.1330
>5265   5268   36.50.1394   0.1769  0.1390
>
> Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#
>
> Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#
> Wrote pdb files with previous and current coordinates
> step 0Warning: 1-4 interaction between 5264 and 5273 at distance 13.965
> which is larger than the 1-4 table size 2.400 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should inc

Re: [gmx-users] so difficult problem

[Amit Choubey]

May be you broke the molecule while using editconf. Try to fix the
periodicity by trjconv and then use it.

On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> I generated my .top and .gro file as drug/enzyme tutorial.
> I used PRODRG to generate them.
> I could pass all of steps in UMbrella sampling tutorial with these
> files,without any warning or error.
> the one thing I changed is rotating box with editconf.
>
>
>
>
> On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey  wrote:
>
>> There is something wrong with your initial configuration. May be you
>> forgot to take care of periodicity, how did you get your initial
>> configuration? Also notice that these kind of problems have been discussed
>> previously.
>>
>> Amit
>>
>> On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour <
>> ramezanpour.moh...@gmail.com> wrote:
>>
>>> Dear All
>>> I am using this .mdp file and I recived the below warnings,I can't solve
>>> that.
>>>
>>>
>>> title= NPT
>>> define   =
>>> integrator   = md
>>> tinit= 0
>>> dt   = 0.002
>>> nsteps   = 50
>>> nstcomm  = 1
>>> comm-grps= protein non-protein
>>> niter= 20
>>> nstxout  = 5000
>>> nstvout  = 5000
>>> nstfout  = 0
>>> nstlog   = 5000
>>> nstenergy= 250
>>> nstxtcout= 250
>>> xtc-precision= 1000
>>> xtc_grps = protein non-protein
>>> energygrps   = Protein  non-protein
>>> nstlist  = 5
>>> ns_type  = grid
>>> pbc  = xyz
>>> rlist= 1.4
>>> domain-decomposition = no
>>> coulombtype  = PME
>>> rcoulomb-switch  = 0
>>> rcoulomb = 1.4
>>> epsilon-r= 1
>>> vdw-type = Cut-off
>>> rvdw-switch  = 0
>>> rvdw = 1.4
>>> DispCorr = EnerPres
>>> fourierspacing   = 0.12
>>> fourier_nx   = 0
>>> fourier_ny   = 0
>>> fourier_nz   = 0
>>> pme_order= 4
>>> ewald_rtol   = 1e-05
>>> epsilon_surface  = 0
>>> optimize_fft = no
>>> tcoupl   = Nose-hoover
>>> tc-grps  = Protein non-protein
>>> tau_t= 0.1  0.1
>>> ref_t= 300  300
>>> Pcoupl   = Parrinello-Rahman
>>> Pcoupltype   = Isotropic
>>> tau_p= 1.0
>>> compressibility  = 4.5e-5
>>> ref_p= 1.0
>>> annealing= no
>>> gen_vel  = yes
>>> gen_temp = 310
>>> gen_seed = 173529
>>> constraints  = all-bonds
>>> constraint-algorithm = Lincs
>>> unconstrained-start  = no
>>> lincs-order  = 4
>>> lincs-warnangle  = 30
>>> morse= no
>>>
>>> my sytem is protein-ligand,I want to generate a NPT.
>>> the result was:
>>>
>>> Step 0, time 0 (ps)  LINCS WARNING
>>> relative constraint deviation after LINCS:
>>> rms 0.002537, max 0.119994 (between atoms 5293 and 5294)
>>> bonds that rotated more than 30 degrees:
>>>  atom 1 atom 2  angle  previous, current, constraint length
>>> starting mdrun 'Protein in water'
>>> 50 steps,   1000.0 ps.
>>>
>>> Step 0, time 0 (ps)  LINCS WARNING
>>> relative constraint deviation after LINCS:
>>> rms 1503.633433, max 55362.878906 (between atoms 5289 and 5290)
>>> bonds that rotated more than 30 degrees:
>>>  atom 1 atom 2  angle  previous, current, constraint length
>>>5264   5263   41.70.1143   0.1261  0.1140
>>>5293   5294   82.70.1221 2612.9744  0.1090
>>>5291   5293   77.20.1517 6082.6147  0.1390
>>>5291   5292  101.00.1117 1518.6106  0.1090
>>>5289   5291   87.70.1353 6891.8911  0.1390
>>>5289   5290  

Re: [gmx-users] so difficult problem

[Amit Choubey]

Could you post the exact command lines ?

On Tue, Jan 4, 2011 at 1:38 AM, mohsen ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> please let me know more.
> I am new with gromacs.
> did I understand correctly?You say me to use from trjconv at first and then
> from editconf?
>  I want to keep fix my molecule and rotate my box to locate in awanted
> direction.
> waht can I do?
> because when I rotate the box my molecule totally is located out of box,but
> protein and ligand are connected as the first state and I think my molecule
> has not broken.
> Thanks in advance
>
>
> On Tue, Jan 4, 2011 at 12:56 PM, Amit Choubey  wrote:
>
>> May be you broke the molecule while using editconf. Try to fix the
>> periodicity by trjconv and then use it.
>>
>>
>> On Tue, Jan 4, 2011 at 1:14 AM, mohsen ramezanpour <
>> ramezanpour.moh...@gmail.com> wrote:
>>
>>> I generated my .top and .gro file as drug/enzyme tutorial.
>>> I used PRODRG to generate them.
>>> I could pass all of steps in UMbrella sampling tutorial with these
>>> files,without any warning or error.
>>> the one thing I changed is rotating box with editconf.
>>>
>>>
>>>
>>>
>>> On Tue, Jan 4, 2011 at 12:38 PM, Amit Choubey wrote:
>>>
>>>> There is something wrong with your initial configuration. May be you
>>>> forgot to take care of periodicity, how did you get your initial
>>>> configuration? Also notice that these kind of problems have been discussed
>>>> previously.
>>>>
>>>> Amit
>>>>
>>>> On Tue, Jan 4, 2011 at 12:33 AM, mohsen ramezanpour <
>>>> ramezanpour.moh...@gmail.com> wrote:
>>>>
>>>>> Dear All
>>>>> I am using this .mdp file and I recived the below warnings,I can't
>>>>> solve that.
>>>>>
>>>>>
>>>>> title= NPT
>>>>> define   =
>>>>> integrator   = md
>>>>> tinit= 0
>>>>> dt   = 0.002
>>>>> nsteps   = 50
>>>>> nstcomm  = 1
>>>>> comm-grps= protein non-protein
>>>>> niter= 20
>>>>> nstxout  = 5000
>>>>> nstvout  = 5000
>>>>> nstfout  = 0
>>>>> nstlog   = 5000
>>>>> nstenergy= 250
>>>>> nstxtcout= 250
>>>>> xtc-precision= 1000
>>>>> xtc_grps = protein non-protein
>>>>> energygrps   = Protein  non-protein
>>>>> nstlist  = 5
>>>>> ns_type  = grid
>>>>> pbc  = xyz
>>>>> rlist= 1.4
>>>>> domain-decomposition = no
>>>>> coulombtype  = PME
>>>>> rcoulomb-switch  = 0
>>>>> rcoulomb = 1.4
>>>>> epsilon-r= 1
>>>>> vdw-type = Cut-off
>>>>> rvdw-switch  = 0
>>>>> rvdw = 1.4
>>>>> DispCorr = EnerPres
>>>>> fourierspacing   = 0.12
>>>>> fourier_nx   = 0
>>>>> fourier_ny   = 0
>>>>> fourier_nz   = 0
>>>>> pme_order= 4
>>>>> ewald_rtol   = 1e-05
>>>>> epsilon_surface  = 0
>>>>> optimize_fft = no
>>>>> tcoupl   = Nose-hoover
>>>>> tc-grps  = Protein non-protein
>>>>> tau_t= 0.1  0.1
>>>>> ref_t= 300  300
>>>>> Pcoupl   = Parrinello-Rahman
>>>>> Pcoupltype   = Isotropic
>>>>> tau_p= 1.0
>>>>> compressibility  = 4.5e-5
>>>>> ref_p= 1.0
>>>>> annealing= no
>>>>> gen_vel  = yes
>>>>> gen_temp = 310
>>>>> gen_seed = 173529
>>>>> constraints  = all-bonds
>>>>> constraint-algorith

Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

[Amit Choubey]

try the -type option with dihedral

amit

On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous  wrote:

> Hi Everyone,
>
> Please I'm trying to calculate one dihedral angle as a function of time
> during my simulation.
> For this, I used g_angle. In the manual (version 4.0.3) it says: the
> indexfile should contain atom-triplets or atom-quadruplets for dihedrals.
>
> I put an atom-quadruplet in my index file, but when I run
> g_angle -f .xtc -n .ndx -od .xvg
>
> and I select the group of atom-quadruplets, gromacs crashes and shows this
> error message:
> number of index elements not multiple of 3, these can not be angle triplets
>
> So actually g_angle only calculates angles not dihedrals?
>
> Thanks
>
> Carla
>
>
> --
> 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
>
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Re: [gmx-users] number of index elements not multiple of 3, these can not be angle triplet

[Amit Choubey]

Yes -ov does give you average angle as a function of time. I am not sure if
this answers your question though.

amit

On Fri, Jan 7, 2011 at 2:40 AM, Carla Jamous  wrote:

> Thank you,
>
> It worked, one last question. Something is not very clear to me:
>
> -ov: plots the average angle of a group of angles as a function of time!!
> What does it mean?
>
> Because I'm getting positive and negative values in the same plot. Are
> these values the values of my dihedral angle as a function of time?
>
> Thanks again,
> Carla
>
>
> On Fri, Jan 7, 2011 at 11:30 AM, Amit Choubey  wrote:
>
>> try the -type option with dihedral
>>
>> amit
>>
>> On Fri, Jan 7, 2011 at 2:16 AM, Carla Jamous wrote:
>>
>>> Hi Everyone,
>>>
>>> Please I'm trying to calculate one dihedral angle as a function of time
>>> during my simulation.
>>> For this, I used g_angle. In the manual (version 4.0.3) it says: the
>>> indexfile should contain atom-triplets or atom-quadruplets for dihedrals.
>>>
>>> I put an atom-quadruplet in my index file, but when I run
>>> g_angle -f .xtc -n .ndx -od .xvg
>>>
>>> and I select the group of atom-quadruplets, gromacs crashes and shows
>>> this error message:
>>> number of index elements not multiple of 3, these can not be angle
>>> triplets
>>>
>>> So actually g_angle only calculates angles not dihedrals?
>>>
>>> Thanks
>>>
>>> Carla
>>>
>>>
>>> --
>>>
>>> gmx-users mailing listgmx-users@gromacs.org
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>>
>>
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Re: [gmx-users] trjconv with multiple chains

[Amit Choubey]

Make your box bigger?

2011/1/6 yuanyuan wang 

> dear all,
>  I am doing a simulation that have many chains in a box , and I can
> find a center for them after serval tries.
>  I use almost every option of trjconv,-pbc
> mol,atom,res,whole,nojump , -ur compact, -center , -box to got bigger box,
> and -boxcenter, -fit ..
>  still some chain cannot convert into box. them jump from one box
> to another ,
>  is there any ways that they not jump to another box?
>  thanks a lot.
>
>
> yuanyuan
>
>
>
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Re: [gmx-users] Energy minimization

[Amit Choubey]

Can you provide more details ? Which graph are you talking about ?

Amit

On Mon, Jan 17, 2011 at 12:05 AM, bharat gupta wrote:

> Hi all,
>
> I am minimizing my protein (230 amino acids)  with the minim.mdp file given
> in the lysozyme tutorial but I am not getting a stable graph .. I checked
> the manual also to look for parameters but I am not able to find such
> information there apart from the theory about the minimzation algos and
> process.. So can anybody direct me to some relevant link or help me out in
> this regard ??
>
>
>
> --
> 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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Re: [gmx-users] Energy minimization

[Amit Choubey]

OK what seemed wrong to you?

On Mon, Jan 17, 2011 at 12:24 AM, bharat gupta wrote:

> I am doin the first minimization step.. here are the details of minim.mdp
> file
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep  ; Algorithm (steep = steepest descent minimization)
> emtol  = 1000.0   ; Stop minimization when the maximum force < 1000.0
> kJ/mol/nm
> emstep  = 0.01  ; Energy step size
> nsteps  = 5; Maximum number of (minimization) steps to perform
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist  = 1  ; Frequency to update the neighbor list and long range forces
> ns_type  = grid  ; Method to determine neighbor list (simple, grid)
> rlist  = 1.0  ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME  ; Treatment of long range electrostatic interactions
> rcoulomb = 1.0  ; Short-range electrostatic cut-off
> rvdw  = 1.0  ; Short-range Van der Waals cut-off
> pbc  = xyz   ; Periodic Boundary Conditions (yes/no)
>
>
>
> --
> 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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Re: [gmx-users] Energy minimization

[Amit Choubey]

Check your log file to see if the minimization criterion was satisfied ie
the max force is less than emtol.

On Mon, Jan 17, 2011 at 12:29 AM, bharat gupta wrote:

>
> The potential energy graph is not coming parallel to x-axis is getting down
> towars the x-axis .. normally it should be paralle to x-axis..
>
> --
> 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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[gmx-users] spurious forces while doing pulling simulation

[Amit Choubey]

Hi all,

I am trying to do pulling simulation. Following are the pull parameters

pull = umbrella
pull_geometry = direction
pull_vec1 = 0 0 1
pull_group1 = RNA
pull_rate1 = 0.01
pull_k1 = 1000
pull_start = yes

Everything works fine until the pull group COM reaches half the box length.
The COM position changes by the box length and that causes huge force on the
group. What should i do to fix this ? Also i am using NPT coupling.

Amit
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Re: [gmx-users] spurious forces while doing pulling simulation

[Amit Choubey]

Hi,

Initially, the pull group center of mass is at 8.16 nm and i want to pull 15
nm. I started with a box size of 37 nm in the pull direction.

The problem occurs when the COM is at 18.5 nm (ie at half the box length).

Thanks for the attention.

Amit

On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi all,
>>
>> I am trying to do pulling simulation. Following are the pull parameters
>>
>> pull = umbrella
>> pull_geometry = direction
>> pull_vec1 = 0 0 1
>> pull_group1 = RNA
>> pull_rate1 = 0.01
>> pull_k1 = 1000
>> pull_start = yes
>>
>> Everything works fine until the pull group COM reaches half the box
>> length. The COM position changes by the box length and that causes huge
>> force on the group. What should i do to fix this ? Also i am using NPT
>> coupling.
>>
>>
> You have to use a sufficiently large box, otherwise the periodic distance
> becomes the reference distance when this happens.  This has been discussed
> numerous times on the list (hint: there is an archive for a reason!) and in
> the tutorial linked here:
>
>
> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
>
> -Justin
>
>  Amit
>>
>>
> --
> 
>
> 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
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Re: [gmx-users] spurious forces while doing pulling simulation

[Amit Choubey]

Hi,

I am still not able to see the reason for the periodic distances coming into
picture.

Also, why pull_geometry = direction_periodic cannot be used with P-coupling;
although it seems to do what i want.

Amit

On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey  wrote:

> Hi,
>
> Initially, the pull group center of mass is at 8.16 nm and i want to pull
> 15 nm. I started with a box size of 37 nm in the pull direction.
>
> The problem occurs when the COM is at 18.5 nm (ie at half the box length).
>
> Thanks for the attention.
>
> Amit
>
> On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul wrote:
>
>>
>>
>> Amit Choubey wrote:
>>
>>> Hi all,
>>>
>>> I am trying to do pulling simulation. Following are the pull parameters
>>>
>>> pull = umbrella
>>> pull_geometry = direction
>>> pull_vec1 = 0 0 1
>>> pull_group1 = RNA
>>> pull_rate1 = 0.01
>>> pull_k1 = 1000
>>> pull_start = yes
>>>
>>> Everything works fine until the pull group COM reaches half the box
>>> length. The COM position changes by the box length and that causes huge
>>> force on the group. What should i do to fix this ? Also i am using NPT
>>> coupling.
>>>
>>>
>> You have to use a sufficiently large box, otherwise the periodic distance
>> becomes the reference distance when this happens.  This has been discussed
>> numerous times on the list (hint: there is an archive for a reason!) and in
>> the tutorial linked here:
>>
>>
>> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
>>
>> -Justin
>>
>>  Amit
>>>
>>>
>> --
>> 
>>
>> 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
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>>
>
>
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Re: [gmx-users] spurious forces while doing pulling simulation

[Amit Choubey]

Yes Justin i understand that. Heres what i think is going on

I dont have any reference group. Now the COM distance is calculated wrt the
origin and whenever the COM is more than half of the box its causing
problem.

I think changing the absolute reference to the initial COM of the pull group
(using pull_init1) should fix this issue but i am not confident.

Thanks for looking into this.

On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi,
>> I am still not able to see the reason for the periodic distances coming
>> into picture.
>>
>>
> I guess I don't fully understand your procedure.  If you only want to pull
> to a COM separation of 15 nm, there should be no problem, but yet you're
> achieving a COM separation of 18.5 nm?  That's exactly the problem.  If your
> box is 37 nm, 18.5 nm corresponds to the transition at which the code
> utilizes either the unit cell distance or the periodic distance as the
> restraint distance.  So it is as this point that your forces go haywire.
>
> -Justin
>
>  Also, why pull_geometry = direction_periodic cannot be used with
>> P-coupling; although it seems to do what i want.
>>
>> Amit
>>
>> On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey > kgp.a...@gmail.com>> wrote:
>>
>>Hi,
>>
>>Initially, the pull group center of mass is at 8.16 nm and i want to
>>pull 15 nm. I started with a box size of 37 nm in the pull direction.
>>The problem occurs when the COM is at 18.5 nm (ie at half the box
>>length).
>>
>>Thanks for the attention.
>>
>>Amit
>>
>>On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul ><mailto:jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>Hi all,
>>
>>I am trying to do pulling simulation. Following are the pull
>>parameters
>>
>>pull = umbrella
>>pull_geometry = direction
>>pull_vec1 = 0 0 1
>>pull_group1 = RNA
>>pull_rate1 = 0.01
>>pull_k1 = 1000
>>pull_start = yes
>>
>>Everything works fine until the pull group COM reaches half
>>the box length. The COM position changes by the box length
>>and that causes huge force on the group. What should i do to
>>fix this ? Also i am using NPT coupling.
>>
>>
>>You have to use a sufficiently large box, otherwise the periodic
>>distance becomes the reference distance when this happens.  This
>>has been discussed numerous times on the list (hint: there is an
>>archive for a reason!) and in the tutorial linked here:
>>
>>
>> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
>>
>>-Justin
>>
>>Amit
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>><mailto: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
>><mailto:gmx-users-requ...@gromacs.org>.
>>
>>Can't post? 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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Re: [gmx-users] spurious forces while doing pulling simulation

[Amit Choubey]

It seems that i cannot figure out a way to change the absolute reference
point (Its the origin by default).

Amit

On Mon, Jan 17, 2011 at 5:52 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Yes Justin i understand that. Heres what i think is going on
>>
>> I dont have any reference group. Now the COM distance is calculated wrt
>> the origin and whenever the COM is more than half of the box its causing
>> problem.
>>
>>
> Correct.
>
>
>  I think changing the absolute reference to the initial COM of the pull
>> group (using pull_init1) should fix this issue but i am not confident.
>>
>>
> Using a defined reference group is the better method.  That way, the pull
> distance is calculated with respect to this reference, and it sounds like
> that will allow you to use the box you have already set up.
>
> -Justin
>
>  Thanks for looking into this.
>>
>> On Mon, Jan 17, 2011 at 5:36 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>Hi,
>>
>>I am still not able to see the reason for the periodic distances
>>coming into picture.
>>
>>
>>I guess I don't fully understand your procedure.  If you only want
>>to pull to a COM separation of 15 nm, there should be no problem,
>>but yet you're achieving a COM separation of 18.5 nm?  That's
>>exactly the problem.  If your box is 37 nm, 18.5 nm corresponds to
>>the transition at which the code utilizes either the unit cell
>>distance or the periodic distance as the restraint distance.  So it
>>is as this point that your forces go haywire.
>>
>>-Justin
>>
>>Also, why pull_geometry = direction_periodic cannot be used with
>>P-coupling; although it seems to do what i want.
>>
>>Amit
>>
>>On Mon, Jan 17, 2011 at 1:04 PM, Amit Choubey
>>mailto:kgp.a...@gmail.com>
>><mailto:kgp.a...@gmail.com <mailto:kgp.a...@gmail.com>>> wrote:
>>
>>   Hi,
>>
>>   Initially, the pull group center of mass is at 8.16 nm and i
>>want to
>>   pull 15 nm. I started with a box size of 37 nm in the pull
>>direction.
>>   The problem occurs when the COM is at 18.5 nm (ie at half the
>> box
>>   length).
>>
>>   Thanks for the attention.
>>
>>   Amit
>>
>>   On Mon, Jan 17, 2011 at 11:40 AM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>>   <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
>>
>>
>>
>>   Amit Choubey wrote:
>>
>>   Hi all,
>>
>>   I am trying to do pulling simulation. Following are
>>the pull
>>   parameters
>>
>>   pull = umbrella
>>   pull_geometry = direction
>>   pull_vec1 = 0 0 1
>>   pull_group1 = RNA
>>   pull_rate1 = 0.01
>>   pull_k1 = 1000
>>   pull_start = yes
>>
>>   Everything works fine until the pull group COM
>>reaches half
>>   the box length. The COM position changes by the box
>>length
>>   and that causes huge force on the group. What should
>>i do to
>>   fix this ? Also i am using NPT coupling.
>>
>>
>>   You have to use a sufficiently large box, otherwise the
>>periodic
>>   distance becomes the reference distance when this
>>happens.  This
>>   has been discussed numerous times on the list (hint:
>>there is an
>>   archive for a reason!) and in the tutorial linked here:
>>
>>
>> http://www.gromacs.org/Documentation/Tutorials#Pull_Code_and_Umbrella_Sampling
>>
>>   -Justin
>>
>>   Amit
>>
>>
>>   -- 
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu <http://vt.edu> <h

[gmx-users] saving velocities and coordinates frequently

[Amit Choubey]

Hi ,

I wish to save velocities and coordinates every step for my system. For
saving disk space i dont want to save water molecules. How can i do this ?

Amit
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[gmx-users] diffusion coefficient

[Amit Choubey]

Hi Everyone,

I have been trying to calculate diffusion coefficient for water. I am trying
to reproduce the numbers published in journal papers.
I am using SPCE water model. I use the g_msd analysis tool.

g_msd -f traj.trr -n index.ndx -s npt.tpr -b 2 -e 8

I use a box of volume 6x6x6 nm^3 which has 7161 water molecules. I
equilibriate the system for a ns and then run for additional 10 ps for
analysis. Here are some of the numbers that i get

a. With Berendsen's T coupling and P coupling on i get 4.4941 (+/-
0.2992) 1e-5 cm^2/s
b. With Berendsen's T coupling on and P coupling off I get 3.2469 (+/-
0.1076) 1e-5 cm^2/s
c. With Berendsen's T coupling on and P coupling off for 1ns and then T,P
coupling both off (for analysis part) i get 2.8085 (+/- 0.0310) 1e-5 cm^2/s
.

c is closest to the widely accepted experimental value of 2.3 1e-5 cm^2/s
but its not quite right.

Could someone explain to me why the values obtained in above 3 cases are
widely different and may be give some tips about the right procedure to
calculate diffusion (method and invoking the g_msd tool)?

Thank you
Amit
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[gmx-users] pbc option

[Amit Choubey]

Hi Everyone,

I changed the gromacs source code a little bit and this change introduced
some bias along x direction. Now i want to do a 'yz' pbc but gromacs has the
option of pbc = xy only. Is there a quick tip to circumvent? I can always
introduce the bias along z but its a little time taking job :)

Amit
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[gmx-users] domain decomposition and load balancing

[Amit Choubey]

Hi Everyone,

I am trying to run a simulation with the option "pbc=xy" turned on. I am
using 64 processors for the simulation. The mdrun_mpi evokes the following
error message before starting the md steps

There is no domain decomposition for 64 nodes that is compatible with the
given box and a minimum cell size of 0.889862 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

This has to do with the load balancing in the domain decomposition version
of mdrun. Can anyone suggest me how to set the option -rdd or -dds?

Also the simulation runs fine on one node (with domain decomposition) and
with particle decomposition but both of them extremely slow.


Thank you,
Amit
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Re: [gmx-users] domain decomposition and load balancing

[Amit Choubey]

Hi Mark,

I am not using PME calculation.

I was hoping mdrun will do the cell allocation itself.

Thanks,
Amit


On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham wrote:

> - Original Message -
> From: Amit Choubey 
> Date: Saturday, February 20, 2010 8:51
> Subject: [gmx-users] domain decomposition and load balancing
> To: Discussion list for GROMACS users 
>
> > Hi Everyone,
> > I am trying to run a simulation with the option "pbc=xy" turned on. I am
> using 64 processors for the simulation. The mdrun_mpi evokes the following
> error message before starting the md steps
> >
> > There is no domain decomposition for 64 nodes that is compatible with the
> given box and a minimum cell size of 0.889862 nm> Change the number of nodes
> or mdrun option -rdd or -dds>
> Look in the log file for details on the domain decomposition>
> > This has to do with the load balancing in the domain decomposition
> version of mdrun. Can anyone suggest me how to set the option -rdd or -dds?
>
> Those options are not normally the problem - but see the log file for info
> and mdrun -h for instructions.
>
> You should read up in the manual about domain decomposition, and see about
> choosing npme such that 64-npme is a number that is suitably composite that
> you can make a reasonably compact 3D grid so that the minimum cell size is
> not a constraint. Cells have to be large enough that all nonbonded
> interactions can be resolved in consultation with at most nearest-neighbour
> cells (and some other constraints).
>
> I'm assuming pbc=xy requires a 2D DD. For example, npme=19 gives npp=45
> gives 9x5x1, but npme=28 gives npp=36 gives 6x6x1, which allows for the
> cells to have the smallest diameter possible. Of course if your simulation
> box is so small that the 2D DD for pbc=xy will always lead to slabs that are
> too small in one dimension then you can't solve this problem with DD.
>
> If pbc=xy permits a 3D DD, then the same considerations apply. npme=19
> gives 5x3x3 but npme=28 allows 4x3x3
>
> > Also the simulation runs fine on one node (with domain decomposition) and
> with particle decomposition but both of them extremely slow.>
>
> Well, that's normal...
>
> Mark
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] domain decomposition and load balancing

[Amit Choubey]

Hi Mark,

I dont think i need to play with npme at all.

Amit

On Fri, Feb 19, 2010 at 2:41 PM, Amit Choubey  wrote:

> Hi Mark,
>
> I am not using PME calculation.
>
> I was hoping mdrun will do the cell allocation itself.
>
> Thanks,
> Amit
>
>
> On Fri, Feb 19, 2010 at 2:27 PM, Mark Abraham wrote:
>
>> - Original Message -
>> From: Amit Choubey 
>> Date: Saturday, February 20, 2010 8:51
>> Subject: [gmx-users] domain decomposition and load balancing
>> To: Discussion list for GROMACS users 
>>
>> > Hi Everyone,
>> > I am trying to run a simulation with the option "pbc=xy" turned on. I am
>> using 64 processors for the simulation. The mdrun_mpi evokes the following
>> error message before starting the md steps
>> >
>> > There is no domain decomposition for 64 nodes that is compatible with
>> the given box and a minimum cell size of 0.889862 nm> Change the number of
>> nodes or mdrun option -rdd or -dds>
>> Look in the log file for details on the domain decomposition>
>> > This has to do with the load balancing in the domain decomposition
>> version of mdrun. Can anyone suggest me how to set the option -rdd or -dds?
>>
>> Those options are not normally the problem - but see the log file for info
>> and mdrun -h for instructions.
>>
>> You should read up in the manual about domain decomposition, and see about
>> choosing npme such that 64-npme is a number that is suitably composite that
>> you can make a reasonably compact 3D grid so that the minimum cell size is
>> not a constraint. Cells have to be large enough that all nonbonded
>> interactions can be resolved in consultation with at most nearest-neighbour
>> cells (and some other constraints).
>>
>> I'm assuming pbc=xy requires a 2D DD. For example, npme=19 gives npp=45
>> gives 9x5x1, but npme=28 gives npp=36 gives 6x6x1, which allows for the
>> cells to have the smallest diameter possible. Of course if your simulation
>> box is so small that the 2D DD for pbc=xy will always lead to slabs that are
>> too small in one dimension then you can't solve this problem with DD.
>>
>> If pbc=xy permits a 3D DD, then the same considerations apply. npme=19
>> gives 5x3x3 but npme=28 allows 4x3x3
>>
>> > Also the simulation runs fine on one node (with domain decomposition)
>> and with particle decomposition but both of them extremely slow.>
>>
>> Well, that's normal...
>>
>> Mark
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>>
>
>
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Re: [gmx-users] domain decomposition and load balancing

[Amit Choubey]

Hi Mark and Justin,

I am using a box of size (20nm)x(20nm)x(60nm)..system is open along z ie
(60nm) side.

I tried using only two nodes, it gives the same error

There is no domain decomposition for 2 nodes that is compatible with the
given box and a minimum cell size of 0.889862 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

Amit

On Fri, Feb 19, 2010 at 3:16 PM, Mark Abraham wrote:

> - Original Message -
> From: "Justin A. Lemkul" 
> Date: Saturday, February 20, 2010 10:13
> Subject: Re: [gmx-users] domain decomposition and load balancing
> To: Discussion list for GROMACS users 
>
> >
> >
> > Amit Choubey wrote:
> > >Hi Mark,
> > >
> > >I am not using PME calculation.
> > >
> > >I was hoping mdrun will do the cell allocation itself.
> > >
> >
> > It will, unless it can't, which is exactly your problem.
> > Mark's point stands, regardless of whether or not you're using
> > PME.  DD requires certain minimum size requirements (which
> > are discussed in the manual and the Gromacs 4 paper), so you
> > have two choices:
> >
> > 1. Read about the options mdrun is telling you about.
> > 2. Use fewer nodes so that the DD algorithm can construct
> > reasonably-sized domains.
>
> 3. Use a larger simulation system so the minimum cell size is larger w.r.t.
> the cutoffs
> 4. (If reasonable) Don't use pbc=xy
>
> Mark
> --
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Re: [gmx-users] domain decomposition and load balancing

[Amit Choubey]

the log file just lists all the parameters of the simulation, following is a
part of it

parameters of the run:
   integrator   = md
   nsteps   = 4000
   init_step= 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 0
   comm_mode= Linear
   nstlog   = 1000
   nstxout  = 1000
   nstvout  = 0
   nstfout  = 500
   nstenergy= 10
   nstxtcout= 0
   init_t   = 0
   delta_t  = 0.002
   xtcprec  = 1000
   nkx  = 0
   nky  = 0
   nkz  = 0
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = FALSE
   ePBC = xy
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = No
   epc  = No
   epctype  = Isotropic
   tau_p= 1
   ref_p (3x3):
  ref_p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress (3x3):
  compress[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord_scaling = No
   posres_com (3):
  posres_com[0]= 0.0e+00
  posres_com[1]= 0.0e+00
  posres_com[2]= 0.0e+00
   posres_comB (3):
  posres_comB[0]= 0.0e+00
  posres_comB[1]= 0.0e+00
  posres_comB[2]= 0.0e+00
   andersen_seed= 815131
   rlist= 1.3
   rtpi = 0.05
   coulombtype  = Reaction-Field-zero
   rcoulomb_switch  = 0
   rcoulomb = 1
   vdwtype  = Shift
   rvdw_switch  = 0.9
   rvdw = 1
   epsilon_r= 1
   epsilon_rf   = inf
   tabext   = 1
   implicit_solvent = No
   gb_algorithm = Still
   gb_epsilon_solvent   = 80
   nstgbradii   = 1
   rgbradii = 2
   gb_saltconc  = 0
   gb_obc_alpha = 1
   gb_obc_beta  = 0.8
   gb_obc_gamma = 4.85
   sa_surface_tension   = 2.092
   DispCorr = No
   free_energy  = no
   init_lambda  = 0
   sc_alpha = 0
   sc_power = 0
   sc_sigma = 0.3
   delta_lambda = 0
   nwall= 0
   wall_type= 9-3
   wall_atomtype[0] = -1
   wall_atomtype[1] = -1
   wall_density[0]  = 0
   wall_density[1]  = 0
   wall_ewald_zfac  = 3
   pull = no
   disre= No
   disre_weighting  = Conservative
   disre_mixed  = FALSE
   dr_fc= 1000
   dr_tau   = 0
   nstdisreout  = 100
   orires_fc= 0
   orires_tau   = 0
   nstorireout  = 100
   dihre-fc = 1000
   em_stepsize  = 0.01
   em_tol   = 10
   niter= 20
   fc_stepsize  = 0
   nstcgsteep   = 1000
   nbfgscorr= 10
   ConstAlg = Lincs
   shake_tol= 0.0001
   lincs_order  = 4
   lincs_warnangle  = 30
   lincs_iter   = 2
   bd_fric  = 0
   ld_seed  = 1993
   cos_accel= 0
   deform (3x3):
  deform[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  deform[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   userint1 = 0
   userint2 = 0
   userint3 = 0
   userint4 = 0
   userreal1= 0
   userreal2= 0
   userreal3= 0
   userreal4= 0
grpopts:
   nrdf:  3.92594e+06
   ref_t:   0
   tau_t:   0
anneal:  No
ann_npoints:   0
   acc:   0   0   0
   nfreeze:   N   N   N
   energygrp_flags[  0]: 0 0
   energygrp_flags[  1]: 0 0
   efield-x:
  n = 0
   efield-xt:
  n = 0
   efield-y:
  n = 0
   efield-yt:
  n = 0
   efield-z:
  n = 0
   efield-zt:
  n = 0
   bQMMM= FALSE
   QMconstraints= 0
   QMMMscheme   = 0
   scalefactor  = 1
qm_opts:
   ngQM = 0


On Fri, Feb 19, 2010 at 3:46 PM, Mark Abraham wrote:

>
>
> - Original Message -
> From: Amit Choubey 
> Date: Saturday, February 20, 2010 10:25
> Subject: Re: [gmx-users] domain decomposition and load balancing
> To: Discussion list for GROMACS users 
>
> > Hi Mark and Justin,
> > I am using a box of size (20nm)x(20nm)x(60nm)..system is open al

[gmx-users] writing forces in gromacs

[Amit Choubey]

Hi everyone,

I had been trying to work with forces of the atoms and stumbled upon
something weird.

In my md.mdp file i ask to write forces with a certain frequency then the
grompp shows a seemingly harmless note, the full md.mdp and extract of the
grompp.out are as follows :-

title   =  Yo
cpp =  /usr/bin/cpp
constraints =  none
integrator  =  md
dt  =  0.002 ; ps !
nsteps  =  8500 ; total 17 ps.
nstcomm =  0
nstxout =  500
nstvout =  500
*nstfout =   500*
nstlog  =  100
nstenergy   =  10
nstlist =  10
ns_type =  grid
rlist   =  1.3
coulombtype=  Reaction-Field-zero
rcoulomb=  1.0
epsilon_rf=  0
vdwtype=  Shift
rvdw=  1.0
rvdw_switch=  0.9
Tcoupl  =  no
energygrps  =   DPPC SOL
Pcoupl  =  no
gen_vel =  no
lincs_iter=   2

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
checking input for internal consistency...
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmx.itp
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxnb.itp
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxbon.itp
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ff_dum.itp
Generated 1369 of the 2211 non-bonded parameter combinations
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/spc.itp
Excluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Opening library file
/home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/aminoacids.dat
Making dummy/rest group for T-Coupling containing 1933647 elements
Making dummy/rest group for Acceleration containing 1933647 elements
Making dummy/rest group for Freeze containing 1933647 elements
Making dummy/rest group for VCM containing 1933647 elements
Number of degrees of freedom in T-Coupling group rest is 3924894.00
Making dummy/rest group for User1 containing 1933647 elements
Making dummy/rest group for User2 containing 1933647 elements
Making dummy/rest group for XTC containing 1933647 elements
Making dummy/rest group for Or. Res. Fit containing 1933647 elements
Making dummy/rest group for QMMM containing 1933647 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 2 element(s): DPPC SOL
Acceleration has 1 element(s): rest
Freeze   has 1 element(s): rest
User1has 1 element(s): rest
User2has 1 element(s): rest
VCM  has 1 element(s): rest
XTC  has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...

*NOTE 1 [file nve.mdp, line unknown]:*
  This run will generate roughly 2493 Mb of data

writing run input file...

There was 1 note

gcq#197: "I Do It All the Time" (Magnapop)

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



Now when i change nstfout to zero (no printing of forces) the note doesnt
show up anymore.

Also for the case with nstfout = 500 it seems that the forces are being read
and written properly, I tried the g_traj tool to see the forces.

Could someone clarify?

Thank you,
Amit Choubey
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Re: [gmx-users] writing forces in gromacs

[Amit Choubey]

Hi Berk.

Thanks a lot. I did not know that.

Amit

On Mon, Feb 22, 2010 at 11:57 PM, Berk Hess  wrote:

>  Hi,
>
> This note is printed when output files will be "large", large is defined as
> more than 2 GB.
> Not writing forces just gets you under this limit.
>
> Berk
>
> --
> Date: Mon, 22 Feb 2010 23:52:13 -0800
> From: kgp.a...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-users] writing forces in gromacs
>
>
> Hi everyone,
>
> I had been trying to work with forces of the atoms and stumbled upon
> something weird.
>
> In my md.mdp file i ask to write forces with a certain frequency then the
> grompp shows a seemingly harmless note, the full md.mdp and extract of the
> grompp.out are as follows :-
>
> title   =  Yo
> cpp =  /usr/bin/cpp
> constraints =  none
> integrator  =  md
> dt  =  0.002 ; ps !
> nsteps  =  8500 ; total 17 ps.
> nstcomm =  0
> nstxout =  500
> nstvout =  500
> *nstfout =   500*
> nstlog  =  100
> nstenergy   =  10
> nstlist =  10
> ns_type =  grid
> rlist   =  1.3
> coulombtype=  Reaction-Field-zero
> rcoulomb=  1.0
> epsilon_rf=  0
> vdwtype=  Shift
> rvdw=  1.0
> rvdw_switch=  0.9
> Tcoupl  =  no
> energygrps  =   DPPC SOL
> Pcoupl  =  no
> gen_vel =  no
> lincs_iter=   2
>
> Ignoring obsolete mdp entry 'title'
> Ignoring obsolete mdp entry 'cpp'
> checking input for internal consistency...
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmx.itp
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxnb.itp
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxbon.itp
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ff_dum.itp
> Generated 1369 of the 2211 non-bonded parameter combinations
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/spc.itp
> Excluding 3 bonded neighbours molecule type 'DPPC'
> Excluding 2 bonded neighbours molecule type 'SOL'
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> initialising group options...
> processing index file...
> Opening library file
> /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/aminoacids.dat
> Making dummy/rest group for T-Coupling containing 1933647 elements
> Making dummy/rest group for Acceleration containing 1933647 elements
> Making dummy/rest group for Freeze containing 1933647 elements
> Making dummy/rest group for VCM containing 1933647 elements
> Number of degrees of freedom in T-Coupling group rest is 3924894.00
> Making dummy/rest group for User1 containing 1933647 elements
> Making dummy/rest group for User2 containing 1933647 elements
> Making dummy/rest group for XTC containing 1933647 elements
> Making dummy/rest group for Or. Res. Fit containing 1933647 elements
> Making dummy/rest group for QMMM containing 1933647 elements
> T-Coupling   has 1 element(s): rest
> Energy Mon.  has 2 element(s): DPPC SOL
> Acceleration has 1 element(s): rest
> Freeze   has 1 element(s): rest
> User1has 1 element(s): rest
> User2has 1 element(s): rest
> VCM  has 1 element(s): rest
> XTC  has 1 element(s): rest
> Or. Res. Fit has 1 element(s): rest
> QMMM has 1 element(s): rest
> Checking consistency between energy and charge groups...
>
> *NOTE 1 [file nve.mdp, line unknown]:*
>   This run will generate roughly 2493 Mb of data
>
> writing run input file...
>
> There was 1 note
>
> gcq#197: "I Do It All the Time" (Magnapop)
>
>  :-)  G  R  O  M  A  C  S  (-:
>
>
>
> Now when i change nstfout to zero (no printing of forces) the note doesnt
> show up anymore.
>
> Also for the case with nstfout = 500 it seems that the forces are being
> read and written properly, I tried the g_traj tool to see the forces.
>
> Could someone clarify?
>
> Thank you,
> Amit Choubey
>
>
> --
> New Windows 7: Simplify what you do everyday. Find the right PC for 
> you.<http://windows.microsoft.com/shop>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please s

[gmx-users] water simulation

[Amit Choubey]

Hi everyone,

I am afraid this is not really a gromacs related question. Could anyone
refer me to a review paper which discusses about simulating water? Does any
of them gives a comparative and complete study of molecular dynamics with
water , answering questions like which water model to use, how to deal with
coulomb interaction, what should be the cutoff value (if cutoff is used) . I
have not been able to find one with complete story. Is anyone aware of such
a publication.

Thank you,
Amit
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[gmx-users] gromacs memory usage

[Amit Choubey]

Hi,

I am having trouble with running gromacs with a large system. I am trying to
use several processors for the md. The error is a memory allocation error
and it might be due to low RAM or large no of particles. I want to know the
detailed memory usage of mdrun ie say for N atoms how much memory does the
master node need and then also whats the memory requirement for the other
nodes. By master node i mean the node that does the domain decomposition
calculation etc during the start of mdrun. A webpage which describes the
memory requirement at various stages during mdrun will be very helpful.

Thank you,
amit
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Re: [gmx-users] Choice of value of rlist, rvdw and rcoulomb

[Amit Choubey]

Hi Lum,

These values have to be chosen very icarefully.
Many artifacts can show up due to poorly chosen cutoff. I would suggest to
get the parameters from a reproducible publication or something.

amit

On Fri, Feb 26, 2010 at 8:49 AM, Lum Nforbi  wrote:

> Hi all,
>
>   Please, can someone let me know if the choice of the value of rlist, rvdw
> and rcoulomb is related to or depends in someway to the distance between
> atoms on a lennard-jones potential plot?
>
> I appreciate your answers.
>
> Lum
>
> --
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Re: [gmx-users] gromacs memory usage

[Amit Choubey]

Hi Mark,

We have few nodes with 64 GB memory and many other with 16 GB of memory. I
am attempting a simulation of around 100 M atoms.

I did find some document which says one need (50bytes)*NATOMS on master
node, also one needs
 (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is this
true?


Thank you,
amit

On Fri, Feb 26, 2010 at 2:57 PM, Mark Abraham wrote:)

> - Original Message -
> From: Amit Choubey 
> Date: Friday, February 26, 2010 20:05
> Subject: [gmx-users] gromacs memory usage
> To: Discussion list for GROMACS users 
>
> > Hi,
> > I am having trouble with running gromacs with a large system. I am trying
> to use several processors for the md. The error is a memory allocation error
> and it might be due to low RAM or large no of particles. I want to know the
> detailed memory usage of mdrun ie say for N atoms how much memory does the
> master node need and then also whats the memory requirement for the other
> nodes. By master node i mean the node that does the domain decomposition
> calculation etc during the start of mdrun. A webpage which describes the
> memory requirement at various stages during mdrun will be very helpful.
>
> The master node does not have a significantly larger memory footprint than
> any other, during setup or the run... For example, a 50K-atom system runs
> fine on 64 BlueGene/L processors with a hard limit of 500MB per processor
> for OS+code+data+MPI.
>
> Does your system run on 1 processor, with and without MPI? How much
> (physical) memory do you have for how large a system?
>
> Mark
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] gromacs memory usage

[Amit Choubey]

>
> Hi Mark,
>
> I quoted the memory usage requirements from a presentation by Berk Hess,
> Following is the link to it
>

http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf


> l. In that presentation on pg 27,28 Berk does talk about memory usage but
> then I am not sure if he referred to any other specific thing.
>
> My system only contains SPC water. I want Berendsen T coupling and Coulomb
> interaction with Reaction Field.
>
> I just want a rough estimate of how big of a system of water can be
> simulated on our super computers.
>
> Thank you,
>
> Amit
>

On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham wrote:

> - Original Message -
> From: Amit Choubey 
> Date: Saturday, February 27, 2010 10:17
> Subject: Re: [gmx-users] gromacs memory usage
> To: Discussion list for GROMACS users 
>
> > Hi Mark,
> > We have few nodes with 64 GB memory and many other with 16 GB of memory.
> I am attempting a simulation of around 100 M atoms.>
>
> Well, try some smaller systems and work upwards to see if you have a limit
> in practice. 50K atoms can be run in less than 32GB over 64 processors. You
> didn't say whether your simulation system can run on 1 processor... if it
> does, then you can be sure the problem really is related to parallelism.
>
> > I did find some document which says one need (50bytes)*NATOMS on master
> node, also one needs
> >  (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute nodes. Is
> this true?>
>
> In general, no. It will vary with the simulation algorithm you're using.
> Quoting such without attributing the source or describing the context is
> next to useless. You also dropped a parenthesis.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] gromacs memory usage

[Amit Choubey]

Hi Mark,

Yes thats one way to go about it. But it would have been great if i could
get a rough estimation.

Thank you.

amit


On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham wrote:

> On 3/03/2010 12:53 PM, Amit Choubey wrote:
>
>>Hi Mark,
>>
>>I quoted the memory usage requirements from a presentation by Berk
>>Hess, Following is the link to it
>>
>>
>>
>> http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
>>
>>l. In that presentation on pg 27,28 Berk does talk about memory
>>usage but then I am not sure if he referred to any other specific
>> thing.
>>
>>My system only contains SPC water. I want Berendsen T coupling and
>>Coulomb interaction with Reaction Field.
>>
>>I just want a rough estimate of how big of a system of water can be
>>simulated on our super computers.
>>
>
> Try increasingly large systems until it runs out of memory. There's your
> answer.
>
> Mark
>
>  On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham > <mailto:mark.abra...@anu.edu.au>> wrote:
>>
>>- Original Message -
>>From: Amit Choubey mailto:kgp.a...@gmail.com>>
>>Date: Saturday, February 27, 2010 10:17
>>Subject: Re: [gmx-users] gromacs memory usage
>>To: Discussion list for GROMACS users ><mailto:gmx-users@gromacs.org>>
>>
>> > Hi Mark,
>> > We have few nodes with 64 GB memory and many other with 16 GB of
>>memory. I am attempting a simulation of around 100 M atoms.>
>>
>>Well, try some smaller systems and work upwards to see if you have a
>>limit in practice. 50K atoms can be run in less than 32GB over 64
>>processors. You didn't say whether your simulation system can run on
>>1 processor... if it does, then you can be sure the problem really
>>is related to parallelism.
>>
>> > I did find some document which says one need (50bytes)*NATOMS on
>>master node, also one needs
>> >  (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute
>>nodes. Is this true?>
>>
>>In general, no. It will vary with the simulation algorithm you're
>>using. Quoting such without attributing the source or describing the
>>context is next to useless. You also dropped a parenthesis.
>>
>>Mark
>>--
>>gmx-users mailing list gmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/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
>><mailto:gmx-users-requ...@gromacs.org>.
>>
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>  --
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> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] gromacs memory usage

[Amit Choubey]

Hi Tsjerk,

I tried to do a test run based on the presentation. But there was a memory
related error (I had given a leverage of more than 2 GB).

I did not understand the 64 bit issue, could you let me know wheres the
documentation? I need to look into that.

Thank you,
amit

On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar  wrote:

> Hi Amit,
>
> I think the presentation gives right what you want: a rough estimate.
> Now as Berk pointed out, to allocate more than 2GB of memory, you need
> to compile in 64bit. Then, if you want to have a real feel for the
> memory usage, there's no other way than trying. But fortunately, the
> memory requirements of a (very) long simulation are equal to that of a
> very short one, so it doesn't need to cost much time.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey  wrote:
> > Hi Mark,
> >
> > Yes thats one way to go about it. But it would have been great if i could
> > get a rough estimation.
> >
> > Thank you.
> >
> > amit
> >
> >
> > On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham 
> > wrote:
> >>
> >> On 3/03/2010 12:53 PM, Amit Choubey wrote:
> >>>
> >>>Hi Mark,
> >>>
> >>>I quoted the memory usage requirements from a presentation by Berk
> >>>Hess, Following is the link to it
> >>>
> >>>
> >>>
> >>>
> http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
> >>>
> >>>l. In that presentation on pg 27,28 Berk does talk about memory
> >>>usage but then I am not sure if he referred to any other specific
> >>> thing.
> >>>
> >>>My system only contains SPC water. I want Berendsen T coupling and
> >>>Coulomb interaction with Reaction Field.
> >>>
> >>>I just want a rough estimate of how big of a system of water can be
> >>>simulated on our super computers.
> >>
> >> Try increasingly large systems until it runs out of memory. There's your
> >> answer.
> >>
> >> Mark
> >>
> >>> On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham  >>> <mailto:mark.abra...@anu.edu.au>> wrote:
> >>>
> >>>- Original Message -
> >>>From: Amit Choubey mailto:kgp.a...@gmail.com>>
> >>>Date: Saturday, February 27, 2010 10:17
> >>>Subject: Re: [gmx-users] gromacs memory usage
> >>>To: Discussion list for GROMACS users  >>><mailto:gmx-users@gromacs.org>>
> >>>
> >>> > Hi Mark,
> >>> > We have few nodes with 64 GB memory and many other with 16 GB of
> >>>memory. I am attempting a simulation of around 100 M atoms.>
> >>>
> >>>Well, try some smaller systems and work upwards to see if you have a
> >>>limit in practice. 50K atoms can be run in less than 32GB over 64
> >>>processors. You didn't say whether your simulation system can run on
> >>>1 processor... if it does, then you can be sure the problem really
> >>>is related to parallelism.
> >>>
> >>> > I did find some document which says one need (50bytes)*NATOMS on
> >>>master node, also one needs
> >>> >  (100+4*(no. of atoms in cutoff)*(NATOMS/nprocs) for compute
> >>>nodes. Is this true?>
> >>>
> >>>In general, no. It will vary with the simulation algorithm you're
> >>>using. Quoting such without attributing the source or describing the
> >>>context is next to useless. You also dropped a parenthesis.
> >>>
> >>>Mark
> >>>--
> >>>gmx-users mailing list gmx-users@gromacs.org
> >>><mailto:gmx-users@gromacs.org>
> >>>http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>>Please search the archive at http://www.gromacs.org/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
> >>><mailto:gmx-users-requ...@gromacs.org>.
> >>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >>>
> >>>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>

Re: [gmx-users] gromacs memory usage

[Amit Choubey]

Hi Roland

I tried 'which mdrun' but it only gives the path name of installation. Is
there any other way to know if the installation is 64 bit ot not?

Thank you,
Amit

On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz  wrote:

> Hi,
>
> do:
> file `which mdrun`
> and it should give:
> /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV),
> dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped
>
> If it is not 64 you need to compile with 64 and have a 64bit kernel. Since
> you asked before about 2GB large files this might indeed be your problem.
>
> Roland
>
> On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey  wrote:
>
>> Hi Tsjerk,
>>
>> I tried to do a test run based on the presentation. But there was a memory
>> related error (I had given a leverage of more than 2 GB).
>>
>> I did not understand the 64 bit issue, could you let me know wheres the
>> documentation? I need to look into that.
>>
>> Thank you,
>> amit
>>
>>
>> On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar wrote:
>>
>>> Hi Amit,
>>>
>>> I think the presentation gives right what you want: a rough estimate.
>>> Now as Berk pointed out, to allocate more than 2GB of memory, you need
>>> to compile in 64bit. Then, if you want to have a real feel for the
>>> memory usage, there's no other way than trying. But fortunately, the
>>> memory requirements of a (very) long simulation are equal to that of a
>>> very short one, so it doesn't need to cost much time.
>>>
>>> Cheers,
>>>
>>> Tsjerk
>>>
>>> On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey  wrote:
>>> > Hi Mark,
>>> >
>>> > Yes thats one way to go about it. But it would have been great if i
>>> could
>>> > get a rough estimation.
>>> >
>>> > Thank you.
>>> >
>>> > amit
>>> >
>>> >
>>> > On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham 
>>> > wrote:
>>> >>
>>> >> On 3/03/2010 12:53 PM, Amit Choubey wrote:
>>> >>>
>>> >>>Hi Mark,
>>> >>>
>>> >>>I quoted the memory usage requirements from a presentation by Berk
>>> >>>Hess, Following is the link to it
>>> >>>
>>> >>>
>>> >>>
>>> >>>
>>> http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
>>> >>>
>>> >>>l. In that presentation on pg 27,28 Berk does talk about memory
>>> >>>usage but then I am not sure if he referred to any other specific
>>> >>> thing.
>>> >>>
>>> >>>My system only contains SPC water. I want Berendsen T coupling and
>>> >>>Coulomb interaction with Reaction Field.
>>> >>>
>>> >>>I just want a rough estimate of how big of a system of water can
>>> be
>>> >>>simulated on our super computers.
>>> >>
>>> >> Try increasingly large systems until it runs out of memory. There's
>>> your
>>> >> answer.
>>> >>
>>> >> Mark
>>> >>
>>> >>> On Fri, Feb 26, 2010 at 3:56 PM, Mark Abraham <
>>> mark.abra...@anu.edu.au
>>> >>> <mailto:mark.abra...@anu.edu.au>> wrote:
>>> >>>
>>> >>>- Original Message -
>>> >>>From: Amit Choubey mailto:kgp.a...@gmail.com
>>> >>
>>> >>>Date: Saturday, February 27, 2010 10:17
>>> >>>Subject: Re: [gmx-users] gromacs memory usage
>>> >>>To: Discussion list for GROMACS users >> >>><mailto:gmx-users@gromacs.org>>
>>> >>>
>>> >>> > Hi Mark,
>>> >>> > We have few nodes with 64 GB memory and many other with 16 GB
>>> of
>>> >>>memory. I am attempting a simulation of around 100 M atoms.>
>>> >>>
>>> >>>Well, try some smaller systems and work upwards to see if you have
>>> a
>>> >>>limit in practice. 50K atoms can be run in less than 32GB over 64
>>> >>>processors. You didn't say whether your simulation system can run
>>> on
>>> >>>1 processor... if it does, then you can be

Re: [gmx-users] gromacs memory usage

[Amit Choubey]

Hi Roland,

It says

gromacs/4.0.5/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64, version
1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared libs), for
GNU/Linux 2.6.9, not stripped

On Tue, Mar 2, 2010 at 10:34 PM, Roland Schulz  wrote:

> Amit,
>
> try the full line (with the "file")
>
> Roland
>
> On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey  wrote:
>
>> Hi Roland
>>
>> I tried 'which mdrun' but it only gives the path name of installation. Is
>> there any other way to know if the installation is 64 bit ot not?
>>
>> Thank you,
>> Amit
>>
>>
>> On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz  wrote:
>>
>>> Hi,
>>>
>>> do:
>>> file `which mdrun`
>>> and it should give:
>>> /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV),
>>> dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped
>>>
>>> If it is not 64 you need to compile with 64 and have a 64bit kernel.
>>> Since you asked before about 2GB large files this might indeed be your
>>> problem.
>>>
>>> Roland
>>>
>>> On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey wrote:
>>>
>>>> Hi Tsjerk,
>>>>
>>>> I tried to do a test run based on the presentation. But there was a
>>>> memory related error (I had given a leverage of more than 2 GB).
>>>>
>>>> I did not understand the 64 bit issue, could you let me know wheres the
>>>> documentation? I need to look into that.
>>>>
>>>> Thank you,
>>>> amit
>>>>
>>>>
>>>> On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar wrote:
>>>>
>>>>> Hi Amit,
>>>>>
>>>>> I think the presentation gives right what you want: a rough estimate.
>>>>> Now as Berk pointed out, to allocate more than 2GB of memory, you need
>>>>> to compile in 64bit. Then, if you want to have a real feel for the
>>>>> memory usage, there's no other way than trying. But fortunately, the
>>>>> memory requirements of a (very) long simulation are equal to that of a
>>>>> very short one, so it doesn't need to cost much time.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Tsjerk
>>>>>
>>>>> On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey 
>>>>> wrote:
>>>>> > Hi Mark,
>>>>> >
>>>>> > Yes thats one way to go about it. But it would have been great if i
>>>>> could
>>>>> > get a rough estimation.
>>>>> >
>>>>> > Thank you.
>>>>> >
>>>>> > amit
>>>>> >
>>>>> >
>>>>> > On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham <
>>>>> mark.abra...@anu.edu.au>
>>>>> > wrote:
>>>>> >>
>>>>> >> On 3/03/2010 12:53 PM, Amit Choubey wrote:
>>>>> >>>
>>>>> >>>Hi Mark,
>>>>> >>>
>>>>> >>>I quoted the memory usage requirements from a presentation by
>>>>> Berk
>>>>> >>>Hess, Following is the link to it
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/berk_csc.pdf
>>>>> >>>
>>>>> >>>l. In that presentation on pg 27,28 Berk does talk about memory
>>>>> >>>usage but then I am not sure if he referred to any other
>>>>> specific
>>>>> >>> thing.
>>>>> >>>
>>>>> >>>My system only contains SPC water. I want Berendsen T coupling
>>>>> and
>>>>> >>>Coulomb interaction with Reaction Field.
>>>>> >>>
>>>>> >>>I just want a rough estimate of how big of a system of water can
>>>>> be
>>>>> >>>simulated on our super computers.
>>>>> >>
>>>>> >> Try increasingly large systems until it runs out of memory. There's
>>>>> your
>>>>> >> answer.
>>>>> >>
>>>>> >> Mark
>>>>> >>
>&g

Re: [gmx-users] gromacs memory usage

[Amit Choubey]

Hi Roland,

I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was
about 154 M particles. This should be feasible according to the numbers.
Assuming that it takes 50bytes per atoms and 1.76 KB per atom per core then

Masternode -> (50*154 M + 8*1.06)bytes ~ 16GB (There is no leverage here)
All other nodes 8*1.06 ~ 8.5 GB

I am planning to try the same run on 64 nodes with 8 cores each again but
not until i am a little more confident. The problem is if gromacs crashes
due to memory it makes the nodes to hang and people have to recycle the
power supply.


Thank you,

amit

On Wed, Mar 3, 2010 at 7:34 AM, Roland Schulz  wrote:

> Hi,
>
> ok then it is compiled in 64bit.
>
> You didn't say how many cores each node has and on how many nodes you want
> to run.
>
> Roland
>
>
> On Wed, Mar 3, 2010 at 4:32 AM, Amit Choubey  wrote:
>
>> Hi Roland,
>>
>> It says
>>
>> gromacs/4.0.5/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD x86-64,
>> version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses shared
>> libs), for GNU/Linux 2.6.9, not stripped
>>
>>
>> On Tue, Mar 2, 2010 at 10:34 PM, Roland Schulz  wrote:
>>
>>> Amit,
>>>
>>> try the full line (with the "file")
>>>
>>> Roland
>>>
>>> On Wed, Mar 3, 2010 at 1:22 AM, Amit Choubey  wrote:
>>>
>>>> Hi Roland
>>>>
>>>> I tried 'which mdrun' but it only gives the path name of installation.
>>>> Is there any other way to know if the installation is 64 bit ot not?
>>>>
>>>> Thank you,
>>>> Amit
>>>>
>>>>
>>>> On Tue, Mar 2, 2010 at 10:03 PM, Roland Schulz  wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> do:
>>>>> file `which mdrun`
>>>>> and it should give:
>>>>> /usr/bin/mdrun: ELF 64-bit LSB executable, x86-64, version 1 (SYSV),
>>>>> dynamically linked (uses shared libs), for GNU/Linux 2.6.15, stripped
>>>>>
>>>>> If it is not 64 you need to compile with 64 and have a 64bit kernel.
>>>>> Since you asked before about 2GB large files this might indeed be your
>>>>> problem.
>>>>>
>>>>> Roland
>>>>>
>>>>> On Wed, Mar 3, 2010 at 12:48 AM, Amit Choubey wrote:
>>>>>
>>>>>> Hi Tsjerk,
>>>>>>
>>>>>> I tried to do a test run based on the presentation. But there was a
>>>>>> memory related error (I had given a leverage of more than 2 GB).
>>>>>>
>>>>>> I did not understand the 64 bit issue, could you let me know wheres
>>>>>> the documentation? I need to look into that.
>>>>>>
>>>>>> Thank you,
>>>>>> amit
>>>>>>
>>>>>>
>>>>>> On Tue, Mar 2, 2010 at 9:14 PM, Tsjerk Wassenaar 
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Amit,
>>>>>>>
>>>>>>> I think the presentation gives right what you want: a rough estimate.
>>>>>>> Now as Berk pointed out, to allocate more than 2GB of memory, you
>>>>>>> need
>>>>>>> to compile in 64bit. Then, if you want to have a real feel for the
>>>>>>> memory usage, there's no other way than trying. But fortunately, the
>>>>>>> memory requirements of a (very) long simulation are equal to that of
>>>>>>> a
>>>>>>> very short one, so it doesn't need to cost much time.
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> Tsjerk
>>>>>>>
>>>>>>> On Wed, Mar 3, 2010 at 5:31 AM, Amit Choubey 
>>>>>>> wrote:
>>>>>>> > Hi Mark,
>>>>>>> >
>>>>>>> > Yes thats one way to go about it. But it would have been great if i
>>>>>>> could
>>>>>>> > get a rough estimation.
>>>>>>> >
>>>>>>> > Thank you.
>>>>>>> >
>>>>>>> > amit
>>>>>>> >
>>>>>>> >
>>>>>>> > On Tue, Mar 2, 2010 at 8:06 PM, Mark Abraham <
>>>>>>> mark.abra...@anu.edu.au>
>>>>>>> > wro

Re: [gmx-users] gromacs memory usage

[Amit Choubey]

Hi Mark and Alexey,

Thank you for taking the time to write the responses. Following is the info
about the cluster

[chou...@hpc-login2 ~]$ uname -a
Linux hpc-login2 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64
x86_64 x86_64 GNU/Linux

[chou...@hpc2000 ~]$ mpiexec --version
Version 0.82, configure options: '--host=x86_64-redhat-linux-gnu'
'--build=x86_64-redhat-linux-gnu' '--target=x86_64-redhat-linux'
'--program-prefix=' '--prefix=/usr' '--exec-prefix=/usr' '--bindir=/usr/bin'
'--sbindir=/usr/sbin' '--sysconfdir=/etc' '--datadir=/usr/share'
'--includedir=/usr/include' '--libdir=/usr/lib64'
'--libexecdir=/usr/libexec' '--localstatedir=/var'
'--sharedstatedir=/usr/com' '--mandir=/usr/share/man'
'--infodir=/usr/share/info' '--with-pbs=/usr/lib64/torque'
'--disable-p4-shmem' 'CFLAGS=-O2 -g' 'build_alias=x86_64-redhat-linux-gnu'
'host_alias=x86_64-redhat-linux-gnu' 'target_alias=x86_64-redhat-linux'

[chou...@hpc2000 ~]$ ifort --version
ifort (IFORT) 10.0 20070426
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.

[chou...@hpc2000 ~]$ icc --version
icc (ICC) 10.0 20070426
Copyright (C) 1985-2007 Intel Corporation.  All rights reserved.


Thanks for all the help.

Amit





2010/3/3 Alexey Shvetsov 

> Hi
>
> Looks like your system simply runs out of memory. So power cycling nodes
> isnt
> needed. If your cluster runs linux then it already has OOM Killer that will
> kill processes that runs out of memory. Also having swap on nodes is a good
> idea even with huge amount  of memory.
> Memory usage for mpi processes will strongly depend on mpi implentation
> because some of them are usualy caching slave process memory (like usualy
> do
> mvapich2)
>
> So can you provide info about youre cluster setup.
> OS version (including kernel version)  uname -a
> mpi version  mpirun --version or mpiexec --version
> also compiler version that was used for compiling gromacs
>
> On Четверг 04 марта 2010 03:15:53 Amit Choubey wrote:
> > Hi Roland,
> >
> > I was using 32 nodes with 8 cores, each with 16 Gb memory. The system was
> > about 154 M particles. This should be feasible according to the numbers.
> > Assuming that it takes 50bytes per atoms and 1.76 KB per atom per core
> then
> >
> > Masternode -> (50*154 M + 8*1.06)bytes ~ 16GB (There is no leverage here)
> > All other nodes 8*1.06 ~ 8.5 GB
> >
> > I am planning to try the same run on 64 nodes with 8 cores each again but
> > not until i am a little more confident. The problem is if gromacs crashes
> > due to memory it makes the nodes to hang and people have to recycle the
> > power supply.
> >
> >
> > Thank you,
> >
> --
> Best Regards,
> Alexey 'Alexxy' Shvetsov
> Petersburg Nuclear Physics Institute, Russia
> Department of Molecular and Radiation Biophysics
> Gentoo Team Ru
> Gentoo Linux Dev
> mailto:alexx...@gmail.com
> mailto:ale...@gentoo.org
> mailto:ale...@omrb.pnpi.spb.ru
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] diffusion coefficient of oxygen molecule

[Amit Choubey]

Hi,

If i remember correctly SPC/E water might be worth trying. There is plenty
of research paper in this field. Try this paper

http://pubs.acs.org/doi/abs/10.1021/jp003020w

Also P,T coupling have effects on Diffusion Coeff.


amit

On Fri, Mar 5, 2010 at 1:29 AM, Sunil Thapa  wrote:

> Respected experts
> I want to calculate the self diffusion cofficient of an oxygen molecule in
> water. The experimental value in the literature is found to be 2.5 x 10-9
> nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off
> Lennard Jones interaction between water and oxygen. I want to reproduce this
> value. In your experience, which model of water would give the closer value.
> I have seen that the self diffusion of SPC and TIP4P waters are 3.8 units
> and 3.2 units whereas the actual value is 2.4 unit. For oxygen the bonding
> potential has been taken to be harmonic. Any knowledge of related literature
> would be helpful because I could not find by googling.
>
> Your idea will really help me.
> Neal
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] How to merge 2 simulation boxes?

[Amit Choubey]

On Thu, Mar 25, 2010 at 9:49 PM, 程迪  wrote:

> Hi, everyone
>
> I have two simulations which could run well separately. Now I want to place
> the box of simulation A onto the box of simulation B. What should I do to
> realise that?
>
> I've tried to copy and paste the .gro and .top file together, but there are
> several mistakes in grompp. I wonder if there are some better method to
> merge 2 simulation boxes.
>

copying straight forward will not help, you have to move the atoms of one of
the box by the box vectors of the other box. Does this make sense ?


>
> Di Cheng
>
> University of Science and Technology of China
> Hefei, Anhui Province 230026
> P. R. China
> E-mail: chen...@mail.ustc.edu.cn
> Tel.: +86-15321055911
>
>
> --
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[gmx-users] pressure for ambient water

[Amit Choubey]

Hi Everyone,

I was doing MD with SPC waters and found something which i am not sure how
to explain.

I made a box of SPC water of dimension 4x4x4 nm^3 and filled with water
using grenbox .

I then did a nvt simulation at 300 K for 1 ns . I used berendsen coupling
and Reaction - Field for coulomb interaction. Cut off were all set to 1
nm. Temperature did converge to 300 K. After this i turned of nvt and did
nve with RF-zero for another ns. Energy was well converged during this (RMSD
< 0.1 %). Temperature was also around 304 K (RMSD < 1%). But the pressure
was 1.1 Kilobar with a fluctuation of 20 % . I don understand this, shouldnt
this be around 1 bar ? Could some one suggest whats on ?

Thank you,
amit
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Re: [gmx-users] pressure for ambient water

[Amit Choubey]

Hi Justin,

Since the density (1 gm/cc) and T (300 K) correspond to ambient condition,
should not the equation of state dictate a pressure around 1 atm?

thank you
amit

On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi Everyone,
>>
>> I was doing MD with SPC waters and found something which i am not sure how
>> to explain.
>>
>> I made a box of SPC water of dimension 4x4x4 nm^3 and filled with water
>> using grenbox .
>>
>> I then did a nvt simulation at 300 K for 1 ns . I used berendsen coupling
>> and Reaction - Field for coulomb interaction. Cut off were all set to 1 nm.
>> Temperature did converge to 300 K. After this i turned of nvt and did nve
>> with RF-zero for another ns. Energy was well converged during this (RMSD <
>> 0.1 %). Temperature was also around 304 K (RMSD < 1%). But the pressure was
>> 1.1 Kilobar with a fluctuation of 20 % . I don understand this, shouldnt
>> this be around 1 bar ? Could some one suggest whats on ?
>>
>>
> Since an NVE ensemble employs neither a thermostat nor a barostat, I don't
> know why you'd expect that.
>
> -Justin
>
>  Thank you,
>> amit
>>
>>
> --
> 
>
> 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/search before posting!
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Re: [gmx-users] pressure for ambient water

[Amit Choubey]

On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>> Hi Justin,
>>
>> Since the density (1 gm/cc) and T (300 K) correspond to ambient condition,
>> should not the equation of state dictate a pressure around 1 atm?
>>
>>
> If the equation of state involves temperature and pressure, yes.


So if you fix the density and temperature shouldnt you land up with right
pressure which we know should be 1 atm.

amit

>
>
>  thank you
>> amit
>>
>>
>> On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>Hi Everyone,
>>
>>I was doing MD with SPC waters and found something which i am
>>not sure how to explain.
>>
>>I made a box of SPC water of dimension 4x4x4 nm^3 and filled
>>with water using grenbox .
>>
>>I then did a nvt simulation at 300 K for 1 ns . I used berendsen
>>coupling and Reaction - Field for coulomb interaction. Cut off
>>were all set to 1 nm. Temperature did converge to 300 K. After
>>this i turned of nvt and did nve with RF-zero for another ns.
>>Energy was well converged during this (RMSD < 0.1 %).
>>Temperature was also around 304 K (RMSD < 1%). But the pressure
>>was 1.1 Kilobar with a fluctuation of 20 % . I don understand
>>this, shouldnt this be around 1 bar ? Could some one suggest
>>whats on ?
>>
>>
>>Since an NVE ensemble employs neither a thermostat nor a barostat, I
>>don't know why you'd expect that.
>>
>>-Justin
>>
>>Thank you,
>>amit
>>
>>
>>-- 
>>
>>Justin A. Lemkul
>>Ph.D. Candidate
>>ICTAS Doctoral Scholar
>>MILES-IGERT Trainee
>>Department of Biochemistry
>>Virginia Tech
>>Blacksburg, VA
>>jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>
>>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/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
>><mailto:gmx-users-requ...@gromacs.org>.
>>
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
> --
> 
>
> 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] pressure for ambient water

[Amit Choubey]

On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>>
>>
>> On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>Hi Justin,
>>
>>Since the density (1 gm/cc) and T (300 K) correspond to ambient
>>condition, should not the equation of state dictate a pressure
>>around 1 atm?
>>
>>
>>If the equation of state involves temperature and pressure, yes.
>>
>> So if you fix the density and temperature shouldnt you land up with right
>> pressure which we know should be 1 atm.
>>
>>
>
> You are not fixing (or conserving) the temperature in an NVE ensemble.
>  That would be an NVT ensemble, employing a thermostat.


I did do NVT first and then for sampling i removed the thermostat. Also as
you mentioned there was not much difference b/n pressure values during NVT
or NVE . The pressure value is as high as 1000 bar in both cases.



> Since instantaneous pressure is calculated (in part) from the kinetic
> energy, and since the kinetic energy is not guaranteed to be conserved, the
> pressure term will also fluctuate accordingly.
>

This is correct. The pressure thus fluctuates about 20 % of the above
mentioned value.

>
> http://www.gromacs.org/Documentation/Terminology/Pressure
>
> The internal energy of the system is constant in an NVE ensemble, the other
> terms may fluctuate as necessary such that all microstates occur with the
> same probability and the energy surface remains flat.


I agree


>  Also recall that an NVE ensemble represents a thermodynamically isolated
> system, not conducting heat or engaging in work with the surrounding system.
>


true


>  So any concept of external pressure and equilibrating the pressure is
> irrelevant.
>

I am not trying to equilibriate the pressure. I am trying to measure the
pressure. I also know that at 300 K and 1gm/cc the P should be 1 bar.

Also, theoretically NVE or NVT are no different than NPT as far as measuring
observables is concerned. Hence i was thinking that if you have the right
volume density and temperature shouldnt you have the right pressure.

>
> -Justin
>
>  amit
>>
>>
>>
>>thank you
>>amit
>>
>>
>>On Sun, May 16, 2010 at 2:07 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
>>
>>
>>
>>   Amit Choubey wrote:
>>
>>   Hi Everyone,
>>
>>   I was doing MD with SPC waters and found something which i
>> am
>>   not sure how to explain.
>>
>>   I made a box of SPC water of dimension 4x4x4 nm^3 and filled
>>   with water using grenbox .
>>
>>   I then did a nvt simulation at 300 K for 1 ns . I used
>>berendsen
>>   coupling and Reaction - Field for coulomb interaction.
>>Cut off
>>   were all set to 1 nm. Temperature did converge to 300 K.
>>After
>>   this i turned of nvt and did nve with RF-zero for another
>> ns.
>>   Energy was well converged during this (RMSD < 0.1 %).
>>   Temperature was also around 304 K (RMSD < 1%). But the
>>pressure
>>   was 1.1 Kilobar with a fluctuation of 20 % . I don
>> understand
>>   this, shouldnt this be around 1 bar ? Could some one suggest
>>   whats on ?
>>
>>
>>   Since an NVE ensemble employs neither a thermostat nor a
>>barostat, I
>>   don't know why you'd expect that.
>>
>>   -Justin
>>
>>   Thank you,
>>   amit
>>
>>
>>   -- 
>>
>>   Justin A. Lemkul
>>   Ph.D. Candidate
>>   ICTAS Doctoral Scholar
>>   MILES-IGERT Trainee
>>   Department of Biochemistry
>>   Virginia Tech
>>   Blacksburg, VA
>>   jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>>
>>231-9080
>>
>>   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>   
>>   -- gmx-users mailing listgmx-users@gromacs.org
>><mailto:gmx-users@gromacs.org>
>>   <mailto:gm

Re: [gmx-users] pressure for ambient water

[Amit Choubey]

On Mon, May 17, 2010 at 6:45 AM, Justin A. Lemkul  wrote:

>
>
> Amit Choubey wrote:
>
>>
>>
>> On Sun, May 16, 2010 at 7:41 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Amit Choubey wrote:
>>
>>
>>
>>On Sun, May 16, 2010 at 5:15 PM, Justin A. Lemkul
>>mailto:jalem...@vt.edu>
>><mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
>>
>>
>>
>>   Amit Choubey wrote:
>>
>>   Hi Justin,
>>
>>   Since the density (1 gm/cc) and T (300 K) correspond to
>>ambient
>>   condition, should not the equation of state dictate a
>>pressure
>>   around 1 atm?
>>
>>
>>   If the equation of state involves temperature and pressure, yes.
>>
>>So if you fix the density and temperature shouldnt you land up
>>with right pressure which we know should be 1 atm.
>>
>>
>>You are not fixing (or conserving) the temperature in an NVE
>>ensemble.  That would be an NVT ensemble, employing a thermostat.
>>
>> I did do NVT first and then for sampling i removed the thermostat. Also as
>> you mentioned there was not much difference b/n pressure values during NVT
>> or NVE . The pressure value is as high as 1000 bar in both cases.
>>
>>
>>Since instantaneous pressure is calculated (in part) from the
>>kinetic energy, and since the kinetic energy is not guaranteed to be
>>conserved, the pressure term will also fluctuate accordingly.
>>
>>
>> This is correct. The pressure thus fluctuates about 20 % of the above
>> mentioned value.
>>
>>
>>http://www.gromacs.org/Documentation/Terminology/Pressure
>>
>>The internal energy of the system is constant in an NVE ensemble,
>>the other terms may fluctuate as necessary such that all microstates
>>occur with the same probability and the energy surface remains flat.
>>
>> I agree
>>
>> Also recall that an NVE ensemble represents a thermodynamically
>>isolated system, not conducting heat or engaging in work with the
>>surrounding system.
>>
>> true
>>
>> So any concept of external pressure and equilibrating the pressure
>>is irrelevant.
>>
>>
>> I am not trying to equilibriate the pressure. I am trying to measure the
>> pressure. I also know that at 300 K and 1gm/cc the P should be 1 bar.
>>
>> Also, theoretically NVE or NVT are no different than NPT as far as
>> measuring observables is concerned. Hence i was thinking that if you have
>> the right volume density and temperature shouldnt you have the right
>> pressure.
>>
>
> I think the disconnect is arising because you're expecting a model of water
> to behave almost like an ideal gas.  The SPC water model, under NPT
> conditions of 300 K and 1 bar, does not give the experimental density of
> water; it is actually somewhat less than 1 g/mL.  So constraining the system
> to fit some pre-conceived notion of the volume to force the density to be
> right conflicts with the properties of the water model itself.  SPC wants to
> be at a lower density, you're forcing it to be at a higher density, all
> while fixing the volume of the simulation cell.  Sounds to me like a recipe
> for high pressure, since SPC wants to expand but you won't let it.
>
> So the starting configuration, assembled with the right density, has not
> properly equilibrated under NPT conditions, yet you are expecting it to do
> so when applying NVE conditions.  I don't know that you'll ever be able to
> satisfy all of these requirements simultaneously unless you can come up with
> a better water model that replicates both ideal and real behavior :)
>

yes model is an issue too. I was just concerned about 3 orders of magnitude
of difference in calculation of pressure. Thank you for the answering.

amit

>
> -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] reading velocity in the g_msd routine

[Amit Choubey]

On Tue, May 18, 2010 at 2:00 PM, Gaurav Goel wrote:

> Hello gmx-users users :)
>
> I am modifying the 'g_msd' utility to be able to calculate viscosities
> using the corresponding Einstein relationship according to equation
> 3.14 in Helfand E., Physical Review, 119, 1, 1960. The equation is
> similar to the mean-square displacement equation for self-diffusion
> coefficient with the position vector 'r_i ' replaced by 'r_ix p_iy'
> where p_iy is the particle momenta in y-direction.
>
> So basically I need to be able to read both position and velocities
> from the trajectory. Presently, gmx_msd.c uses 'read_first_x' and
> 'read_next_x' to read the coordinates. Can you please comment on how I
> can modify this code to read the corresponding velocities?
>

You could write your own little code to do that, see below for reading gro
format

http://manual.gromacs.org/current/online/gro.html

amit

>
> Any help is greatly appreciated.
>
> thanks,
> Gaurav
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Re: [gmx-users] Restarting after NVT: continuation error

[Amit Choubey]

On Tue, May 25, 2010 at 2:32 PM, VANDANA KUMARI <
kumar...@buckeyemail.osu.edu> wrote:

>
> Hello Gromacs Users,
>
> I am trying to make tpr file for NPT equilibration after NVT equilibration
> using
>
> grompp -f npt.mdp -c nvt.gro -t nvt.trr -p topol.top -n index.ndx -o
> npt.tpr
>

> I am using  parameter " continuation = yes " in npt.mdp  for restarting
> after NVT, but I am getting this warning massage:
>

>  WARNING 1 [file npt.mdp, line unknown]:
>   Unknown left-hand 'continuation' in parameter file
>
>
well to continue why dont you use the same velocities ; just say gen_vel =
no

amit

> Please help me with this issue.
>
> Thank you
> --
> Vandana
>
>
>
>
>
>
>
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