On 1/31/13 11:53 AM, George Patargias wrote:
Dear Gromacs list
I would like to ask a question regarding the global rotation and
translation removal in GROMACS.
In my mdp file I use the following options:
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 10
; group(s) for center of mass motion removal
comm-grps =
Are these options ensuring that global rotation and translation is removed
every 10 steps?
More directly, it removes net motion of the center of mass, thus avoiding
problems like the flying ice cube.
Is the trjconv command (as issued below) also removing global rotation and
translation?
trjconv -f traj_Total.xtc -s prod1.tpr -o rot+trans.xtc -fit rot+trans
Not necessarily global motions, but you can apply the fitting to whatever subset
of atoms you like.
In which case is the "-center" option in trjconv is used?
Many. trjconv is sort of a Swiss army knife, capable of doing dozens of things
if the right options are applied. The -center option is probably most often
used to center a simple solute in the box in every frame.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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