VMD-L Mailing List

From: RAKESH (rakeshkrish_at_iitb.ac.in)
Date: Fri Mar 30 2018 - 08:39:40 CDT

Dear all,

I have modelled a protein of 160 amino acids and simulated it for few 100ns
in namd.
Then I coarse grained the system using MARTINI and tried it to further
simulate for some microseconds.

The simulation was running and abruptly got crashed in between during the
production run,
something like this

ERROR: Atom 420 velocity is 25965.1 12571.2 -6373.37 (limit is 1200, atom
35 of 70 on patch 159 pe 17)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
patch 159 pe 17).
ERROR: Exiting prematurely; see error messages above.
ERROR: Atom 496 velocity is -25706.5 -12714.7 6397.55 (limit is 1200, atom
31 of 67 on patch 158 pe 15)
ERROR: Atom 476 velocity is -1050.43 -77.2906 -943.981 (limit is 1200, atom
63 of 67 on patch 158 pe 15)
ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
patch 158 pe 15).

Can someone what is the error ??