[gmx-users] remove center of mass motion

[Justin A. Lemkul]

M. Emal Alekozai wrote:
> Dear All,
> 
> I have a trajectory where the center of mass motion is not removed. In the mdrun.mdp file the option "comm-grps" was commented out:
>    ; mode for center of mass motion removal =
>     comm-mode                = Linear
>    ; number of steps for center of mass motion removal =
>    nstcomm                  = 1
>    ; group(s) for center of mass motion removal =
>    ;comm-grps                = Protein SOL
> 
> How can I remove the center of mass motion form a trajectory which was created with the above settings?
> I found an old posting [1] in the Gromacs mailinglist but no answer to it.
> 
> 1: http://www.gromacs.org/pipermail/gmx-users/2006-November/024751.html

You might find this thread more useful:

http://www.gromacs.org/pipermail/gmx-users/2006-June/022169.html

If you do a search for "center of mass trjconv" you will come up with lots of 
results that suggest using various iterations of trjconv -fit or trjconv -center.

-Justin

> 
> 
> Thanks
> Emal
> 

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Justin A. Lemkul
Graduate Research Assistant
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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