[gmx-users] Simulation crash and Large VCM(group rest)...

[David]

On Thu, 2002-09-05 at 02:01, A. Pandini wrote:
> Hi all,
> 
> I am trying to simulate a small protein (57aa) in a dodecahedron
> box (SPC water) and I am using PME.
> After the first step I got a long list of:
> ------------------------------------------------------------------------
> Large VCM(group rest):     -0.00000,      0.00000,     -0.00000, ekin-cm:
> 0.00000
> Large VCM(group rest):     -0.00000,      0.00000,     -0.00000, ekin-cm:
> 0.00000
> Large VCM(group rest):     -0.00000,      0.00000,     -0.00000, ekin-cm:
> 0.00000
> Large VCM(group rest):     -0.00000,      0.00000,     -0.00000, ekin-cm:
> 0.00000
> Large VCM(group rest):     -0.00000,     -0.00000,     -0.00000, ekin-cm:
> 0.00000
> Large VCM(group rest):     -0.00000,     -0.00000,     -0.00000, ekin-cm:
> 0.00000
> Large VCM(group rest):     -0.00000,     -0.00000,     -0.00000, ekin-cm:
> 0.00000
> Large VCM(group rest):     -0.00000,     -0.00000,     -0.00000, ekin-cm:
> 0.00000
> Large VCM(group rest):     -0.00000,     -0.00000,     -0.00000, ekin-cm:
> 0.00000
> calc_bor: cg0=0, cg1=3594, ncg=3594
> CG0[0]=0, CG1[0]=3594
> CG0[1]=0, CG1[1]=0
> calc_bor: cg0=0, cg1=3594, ncg=3594
> CG0[0]=0, CG1[0]=3594
> CG0[1]=0, CG1[1]=0
> -------------------------------------------------------------------------
> 
> In 2380 steps the simulation crashed.
> 
> I had a look on the archive and found this could be something weird...
> What does this message mean?
> Is due to my starting structure?
> Any suggestion on how to solve the problem?

This could be the PME/tricilinic box bug. Could you try to center the
protein in the box (editconf -c) and start again?

The new gromacs version with this bug fixed will come out *real soon
now*


> 
> Thanks a lot
> Alex
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
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://zorn.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++