[gmx-users] center of mass motion?
David van der Spoel
spoel at xray.bmc.uu.se
Fri Dec 6 15:41:44 CET 2002
On Fri, 2002-12-06 at 12:16, MOLTENI at unisi.it wrote:
> 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?
it is completely normal, and you can use it to compute protein diffusion
you are remving total center of mass motion. you can also use two
groups, protein and rest e.g.
> Thanks in advance
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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