Re: question about running equilibration in NAMD

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Jun 08 2004 - 15:50:28 CDT

This issue has been discussed many times on the list, please search the
list and apply the suggestions given there.

On Tue, 8 Jun 2004 jz7_at_duke.edu wrote:

> 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
>
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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