[gmx-users] Large VCM revisited
Martina Bertsch, PhD
mbe404 at lulu.it.northwestern.edu
Thu Nov 13 09:33:01 CET 2003
My PR-MD simulation on a GPCR model embedded in a POPC bilayer, using
PME, with separate Berendsen T coupling at 300K for each group (GPCR,
POPC and SPC water) and anisotropic p coupling, crashed after only 4
1-fs steps. Upon examining the log file, I found a huge number of
Large VCM(group Protein_POP): -0.00000, 0.00000, -0.00000,
Large VCM(group SOL): -0.00001, 0.00007, 0.00009,
No other warning messages appear.
I know that VCM stands for velocity of the center of mass. I am using
the comm_mode linear and removing the center of mass for the
protein_popc and sol (see the pr.mdp below). How would I know if I have
a strange center of mass group defined? I defined protein_popc by:
make_ndx -f MT1_popc25_postem.gro -o index.ndx
> 1 | 12
My system consists of one protein molecule, 127 POPC molecules and 1459
waters. The starting structure for PR-MD was minimized by 10000 steps of
CG-EM, carrying out SD steps with a frequency nstcgstee=50. After CG,
the potential energy of the system was -2.77798e+05 and the maximum
force was 7.79061e+02.
Your advice will be greatly appreciated.
Martina Bertsch, Ph.D.
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611
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