[gmx-users] Large VCM in position restrained MD
spoel at xray.bmc.uu.se
Wed Sep 25 21:44:45 CEST 2002
On Wed, 2002-09-25 at 21:06, ireena bagai wrote:
> Dear all,
> I carried out a 500 ps(nsteps=500000,
> dt=.001ps) position restrained run on a decaglycine
> molecule in an NVE ensemble(i.e. no temperature or
> pressure coupling used).My run stopped after 19000
> steps(set nstlog=500 in mdp file) with a message
> "Fatal XTC error". When I checked for the disk space,
> I found it was full although when I had started with
> this run, the space in the disk was enough to easily
> accomodate all the trajectory and log files. On
> examining my log file, I found that a huge one was
> being generated in which three-fourth itself was being
> occupied by some erroneous warning:-
> Large VCM (group rest) 0.0000 -0.0000 0.0000
> calc_bor:-cg=0, cg=594, ncg=594.
VCM means velocity of the center of mass. Do you have a strange center
of mass group defined?
> And the temperature in all these steps was shown to be
> very low, around 50K.
If you don't apply T coupling, and you do use PME your temperature will
be almost constant (Erik is working on it to be exactly constant, i.e.
NVE ensemble). There is no default temperature, or T coupling. You
decide. If you use cut-offs without T-coupling your system will heat up,
and after a while it will explode. That could actually give rise to your
problem, check the final temperature.
> Could anyone please suggest, what this error is (what
> does VCM mean) and why is the temperature going so
> low. If we don't use temp. coupling, will it not by
> default run the simulation at 300K. The fluctuation
> would have been understandable if at least the
> temperature at step 0 was 300K but that too is being
> shown to be 2.101455e-02.
> Thanking you so much
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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://zorn.bmc.uu.se/~spoel
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