[gmx-users] shift in trajectory

[Justin Lemkul]

On 10/17/19 5:24 AM, Amin Rouy wrote:
> Dear Justin,
>
> Thank you for detailed answer. However, I am still struggling and none of
> these helped me.

What have you done and what was the outcome? It's impossible to give 
better advice without knowing what specifically is going wrong.

> One thing I concern in traj.tpr file;
>   I run gmx trjconv with Gromcac.5, which requires .tpr file, while I see in
> http://manual.gromacs.org/documentation/2019/onlinehelp/gmx-trjconv.html that
> the file is 'Optional' to provide.

trjconv does a lot of things. Not all of them require a .tpr file, hence 
the "optional" designation. What you're trying to do does require a .tpr 
file because to account for periodicity effects, the bonded connectivity 
of all molecules needs to be known.

-Justin

>
> On Wed, Oct 16, 2019 at 6:05 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 10/16/19 12:00 PM, Patel, Lara Anne wrote:
>>> There is a way to get around the mass being split across the simulation
>> box IF your residue A's are all grouped together from the start.
>>>
>>> First, run the gmx trjconv function with -pbc flag as none.  The
>> trajectory produced will be spread out.  The index group selected should be
>> for the whole of what you will be printing out in your final trajectory.
>>> gmx trjconv -f traj.xtc -o traj1.xtc -pbc none -n index.ndx
>>>
>>>
>>>
>>> Second run the gmx trjconv function with the -center command with an
>> index file that has a group just for residue 'A'.  The index group selected
>> for centering should be for residue A. The program will also ask for what
>> group will be printed to the file (i.e. your system).
>>> gmx trjconv -f traj1.xtc -o traj2.xtc -n index.ndx -center
>>>
>>>
>>>
>>> Third run the gmx trjconv function with the -pbc flag for mol to get
>> everything back within the periodic boundary conditions.  This will only
>> ask for the group that should be printed.
>>> gmx trjconv -f traj2.xtc -o traj2.xtc -n index.ndx -pbc mol
>>>
>>>
>>> You might be able to combine the second and third steps but I find that
>> it is easier just to do this in progressive steps.
>>
>> Making molecules whole should always be the first step. See
>>
>> http://manual.gromacs.org/current/user-guide/terminology.html#suggested-workflow
>>
>> One call to trjconv is all the OP needs, using -pbc mol -center and an
>> index group corresponding to the residue of interest to be chosen for
>> centering.
>>
>> -Justin
>>
>>> Lara
>>>
>>>
>>> ________________________________
>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Amin Rouy
>> <aminrou1986 at gmail.com>
>>> Sent: Wednesday, October 16, 2019 9:19:39 AM
>>> To: gromacs.org_gmx-users at maillist.sys.kth.se; gmx-users at gromacs.org
>>> Subject: [gmx-users] shift in trajectory
>>>
>>> Hi,
>>>
>>> I want to shift my trajectory such that the center of mass of residue 'A'
>>> locates in the center of my rectangular box.
>>>
>>> I have tries all flags in  gmx trjconv, but could not succeed. Any help
>>> would be appreciated.
>>> --
>>> Gromacs Users mailing list
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>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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