[gmx-users] Large VCM in position restrained MD

ireena bagai ireena_b at yahoo.com
Wed Sep 25 21:06:20 CEST 2002

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.

And the temperature in all these steps was shown to be
very low, around 50K.

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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