Dear Ye,
> I followed the tutorial of DNA simulation and perform the
> minimation and md simulation of a acetic acid.
> In the second md step, it stops with the followin error message:
> NSTEP = 11400 TIME(PS) = 42.800 TEMP(K) =
> 297.51 PRESS = -205.3
> Etot = -5006.8792 EKtot = 1129.4954 EPtot
> = -6136.3746
> BOND = 0.7220 ANGLE = 2.2301 DIHED
> = 7.3177
> 1-4 NB = 0.2971 1-4 EEL = -103.9216 VDWAALS
> = 905.0687
> EELEC = -6948.0886 EHBOND = 0.0000 RESTRAINT
> = 0.0000
> EKCMT = 582.8635 VIRIAL = 669.5663 VOLUME
> = 19555.3011
> Density
> = 0.9750
> Ewald error estimate: 0.3798E-04
>
> --------------------------------------------------------------
> ----------------
>
> vlimit exceeded for step 11426 ; vmax = 60309066.7197193
One of your atoms has flown off at a massive speed, probably because it
collided with another atom. It is a little hard to decipher what has
happened from your output file but I suspect the fact that the volume is
large may be a warning sign. Are you running periodic boundaries here? What
have you solvated your acetic acid in?
It seems strange that the calculation suddenly failed after 42ps but perhaps
it had gone wrong earlier. Try setting ntpr=1 and ntwx=1 and then watch the
mdcrd file over a few hundred steps and see if you can see anything wrong.
Without more information, input files etc we cannot help much more I am
afraid.
All the best
Ross
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
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Received on Tue Mar 01 2005 - 16:53:00 PST
