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