Re: ,log and .out files with namd running on mac os x (panther)

From: Brian Bennion (
Date: Fri May 07 2004 - 10:51:14 CDT

Hello Arieana,

I know it has been awhile since you sent the last email, hopefully someone
has helped you out. Just in case though...

I just looked at your config file and have a few questions/hints.

Have you tried turning off the tclforces and IMD sections of your config?

In your log file I see that you have ~1300 atoms, and ~2000 dihedrals and
that some atoms are fixed, however, no memory is being used? That is odd
indeed. Furthermore the charge on the system is greater than 34 electron
units, this might be a little excessive for NAMD.

Have you successfully completed any minimization of this system?


On Wed, 5 May 2004, Arieana Moore wrote:

> For some reason, I can't copy and paste the files so I'll send them as
> attachments. Thanks .

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

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