question about running equilibration in NAMD

From: jz7_at_duke.edu
Date: Tue Jun 08 2004 - 14:25:41 CDT

Dear all,

I am trying to use equilibrate my system after running minimization. But
the log file gave the following error message:

ERROR: Atom 2400 velocity is -1.66485e+06 -2.39887e+06 257201 (limit is
10000)
ERROR: Atom 5301 velocity is 2.31347e+07 3.33347e+07 -3.5742e+06 (limit
is 10000)
ERROR: Atoms moving too fast; simulation has become unstable.
REASSIGNING VELOCITIES AT STEP 4278 TO 310 KELVIN.
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.

etc.

Would you please tell me how to solve this problem?

PS. I made some modification to the topology file and parameter file. Is
 that related to the erroe message?

Thanks a lot!

Sincerely,
Jeny

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