[gmx-users] center of mass motion?

MOLTENI at unisi.it MOLTENI at unisi.it
Fri Dec 6 12:16:39 CET 2002

Dear gmx users,
I am running MD on a peptide in water. Looking at a movie of (a part of)
my trajectory, I see that the molecule is often near the box boundary,
and therefore sometimes jumps in from the opposite side of the box (I
use PBC). I still have to have a look at the complete
trajectory.....but: is it normal for the peptide to be near the box
edge, when at the beginning I put it in the middle? Can it be due to
center of mass motion? Does it make sense? 
I checked my md.mdp file (which I modified from the ones in gromacs
examples) and indeed the keyword "comm_mode" doesn't appear in my file,
but "nstcomm" is = 1 .... does it mean that I'm removing center of mass
motion at every step... or never? (i.e., which is the default value for
Moreover, the manual says that "nstcomm" should be used only for vacuum
simulations? Why? 

Thanks in advance


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