[gmx-users] How to center molecules in the box with trjconv ?

Sat Aug 21 18:48:54 CEST 2010

It works !!!

Thank you Justin

A bientôt 

Stefane

ABEL Stephane 175950 wrote:
> Hi all,
>
> I have simulated a system containing 55 DPC molecules, a peptide some ions
> and water in a cubic box. Initially all molecules were placed randomly in the
> box. As expected during the simulation all the DPC molecules aggregate to
> form a stable micelle with the peptide located at the micelle interface.
>
> Now I would like to plot some MD configs in a PDB format some configs where
> the micelle and the peptide are placed in the center of the box. To take into
> account the PBC and to obtain the PDB, for the last frame at 150 ns as I used
> trjconv with the following commands:
>
> 1-  trjconv_mpi -f traj_KTM17_DPC_all.xtc -s hMRP1_K-TM17_DPC.tpr -pbc nojump
> -b 150000 -e 150000 -o traj_KTM17_DPC_0ns_noJump.pdb
>
> With "non-SOL" (DPC and peptide) as a group for output and where
> traj_KTM17_DPC_all.xtc is the trajectory with *no* PBC transformation
>
> 2-  trjconv_mpi -f traj_KTM17_DPC_0ns_noJump.pdb -s hMRP1_K-TM17_dpc.gro
> -center -o traj_KTM17_DPC_0ns_noJump_center.pdb
>
> With DPC as a group for centering and "System" (DPC and peptide) as a group
> for output. the *.gro file contains only the DPC and peptide.
>
> Unfortunately, these commands do not work since the micelle (and the peptide)
> are not in the box center. I have tried many others commands with -pbc as
> mol, res with no success.
>

I have never had much success using multi-molecule groups for centering or other
correction using trjconv.  Centering on the peptide, i.e. trjconv -pbc mol -ur
compact -center, should do the trick.  I have never found -pbc nojump to work
very well, for a reason that is still unknown to me.

-Justin

> I used GMX version 4.0.7
>
> Any advices would be helpful.
>
> Stefane
>
>

--
========================================

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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Message: 6
Date: Fri, 20 Aug 2010 13:19:54 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] intersting problem
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4C6EB93A.6010400 at vt.edu>
Content-Type: text/plain; charset=UTF-8; format=flowed

babu gokul wrote:
> dear all
> I want to calculate the how many water molecule are their with in 3.5 A
> of a particular atom. could anyone help me in this regard

g_dist -dist

-Justin

> E R Azhagiya singam
>
>

--
========================================

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

========================================

------------------------------

Message: 7
Date: Fri, 20 Aug 2010 21:55:40 +0200
From: XAvier Periole <x.periole at rug.nl>
Subject: Re: [gmx-users] force constants for umbrellla histograms
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <DAAE7E83-E389-4DC8-9E38-517AB08D52FA at rug.nl>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

The most important is that you have to put in trajectories that
are equilibrated! You can mix as much force constant values
you like but always equilibrated ...

Then the lower the force constant the longer the simulation needs
to be to reach equilibrium: larger conformational space accessible.
I can also imagine that a too strong force constant might deform
your molecules in a manner you should not.

>
> Then does it matter how many times you vary it, and how large ?
> In my
> sampling I have very good histograms up to 2 nm (force constant = 1000
> kj/mol), above 2nm they are not. I feel I may have to use a force
> constant of 500 for the next 3 or 4 windows, and even less again 
> (ca~ 50
> kj/mol) beyond that.
>
> Cheers
>
> Gavin
>
>
> XAvier Periole wrote:
>>
>> On Aug 20, 2010, at 5:12 PM, Gavin Melaugh wrote:
>>
>>> Hi all
>>>
>>> Is is O.K to use different force constants for different sampling
>>> windows for the generation of the potential of mean force curves?
>> Yes.
>>>
>>> Many Thanks
>>>
>>> Gavin
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>
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------------------------------

Message: 8
Date: Sat, 21 Aug 2010 11:54:17 +0330
From: leila karami <karami.leila1 at gmail.com>
Subject: [gmx-users] wrong string length 0 for string buf
To: gmx-users <gmx-users at gromacs.org>
Message-ID:
        <AANLkTi=_mMTa=qAkYniTVBynu6OHRdnuNzP18jkD4idL at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi gromacs users

When I uesed command : trjconv -f com_full.xtc -s com_full.tpr -n com.ndx -o
com.xtc -pbc nojump -ur compact -center

gromacs gives me the following error:

Program trjconv, VERSION 4.0.5
Source code file: gmxfio.c, line: 609

Fatal error:
wrong string length 0 for string buf (source tpxio.c, line 1641)

Any suggestions would be greatly appreciated.
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