Re: error in scripting

From: Axel Kohlmeyer (
Date: Tue Feb 16 2010 - 06:28:55 CST

On Tue, Feb 16, 2010 at 6:26 AM, ipsita basu <> wrote:
> Dear all,
>            I have prepared a bilyer in charmm and make psf file in
> xplor format. I want to minimise and then equilibrate it in namd. But
> the job is aborted. My input is attached here and some of the errors
> are given below:

> Can you please suggest me what is the solution of it?  I read such
> problems in namd-mailing list and according to some thread I increase
> pmegridsize. But doing this the job is running for few steps more but
> aborted finally. Please give me some suggestions.

this kind of error message often indicates that your input is of
very high potential energy and some atoms are becoming
too fast. most likely your input geometry is crap and you need
to build it more carefully.

just running minimize for a few steps and then doing production
MD works for small, well behaved peptides. a complex multi-component
system neeeds a far more sophisticated equilibration protocol
to make sure that you don't destroy your setup and have energy
equipartitioning throughout the various components.

several people have commented on this in the past. dig through
the mailing list archives.

>                                   Thanking You
>                                     Ipsita Basu
> --
> Ipsita Basu
> Research Fellow
> c/o : Dr. Chaitali Mukhopadhyay
> Rajabazar Science College
> 92 APC Road
> Kolkata - 700009

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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