[gmx-users] Large VCM revisited

[David van der Spoel]

On Thu, 2003-11-13 at 09:36, Martina Bertsch, PhD wrote:
> 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
> 

actually these numbers are very small. Isn't there any other warning?
Try with mdrun -v -debug

You could also try to start with a short equilibration with position
restraints and without pressure scaling
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 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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