[gmx-users] Large VCM revisited

[Martina Bertsch, PhD]

Dear colleagues,

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 
warnings:  

Large VCM(group Protein_POP):     -0.00000,      0.00000,     -0.00000, 
ekin-cm:      0.00000
Large VCM(group SOL):     -0.00001,      0.00007,      0.00009, 
ekin-cm:      0.00027

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
 > q

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.

Kind regards,

Martina Bertsch, Ph.D.
Northwestern University
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611




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