VMD-L Mailing List

From: Ganesh Kamath (gkamath9173_at_gmail.com)
Date: Wed Aug 22 2012 - 15:16:14 CDT

Hi All,

  This is more like a NAMD problem. However can someone please help. I
generate a polymer
using patch in psfgen and create a polymer of 30-mer with water around it.
There seems to be no error
in the psfgen. I compare the number of bonds, angles and dihedrals
generated with a psf file that
I created without the patch command. They match in the numbers of terms.

However after a minimization of 500 steps, I get this error.

ERROR: Atom 36984 velocity is 15764.9 5102.3 -14461.9 (limit is 14000, atom
755 of 807 on patch 48 pe 2)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
patch 48 pe 2).
ERROR: Exiting prematurely; see error messages above.

Can someone please help?

thanks,
ganesh