Re: "Constrain failure" in NAMD

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon May 10 2004 - 10:47:29 CDT

Hello Micheal,

I looked over your .inp file and I am not familiar with the formatting
your are using, it seems to be a charmm input file not and NAMD file...

In any case your problem lies in the dimenisions of the system you are
modeling. Your bond energy increases to a unrealistic value during the
minimization. This means that at least two bonded atoms are being pulled
apart. The log file does contain a warning to increase the box size.

Have you tried this?

Regards,
Brian

On Sat, 8 May 2004, Michael Chen wrote:

> Hi, Dr. Brian,
>
> Thank you very much for your helps.
> Before you read my cofig file and the log, there are some things I would
> like to tell you:
> 1. In my PSF, I have 0 dihedral angles
> 2. The gradient tolerance was never below 1 no matter how long NAMD ran
> Hope those pieces of information will be helpful, and thank you again
> for your helps.
> May you have a nice weekend.
>
> *****************************************************
> Michael Chen
>
> Department of Biochemistry
> SUNY Upstate Medical University
> 750 East Adams Street
> Syracuse, NY 13210
> USA
> *****************************************************
> >>> Brian Bennion <brian_at_youkai.llnl.gov> 05/07/04 5:40 PM >>>
> Can you send your config file and your log?
>
>
> *****************************************************************
> **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 **
> *****************************************************************
>
>
>

*****************************************************************
**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 **
*****************************************************************

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:35 CST