VMD-L Mailing List

From: Nuno R. L. Ferreira (nunolf_at_ci.uc.pt)
Date: Thu Feb 23 2006 - 05:02:23 CST

Hi Lily

Maybe this question should be put on namd mailing-list ;-)

Usually this kind of error appears when the starting coordinates have atom clashes, confering to those atoms a big VDW repulsion energy.

But you say that the coordinates came from a previous md run. Are you sure you're giving to namd the correct velocities/coordinate files?

Try to do a EM on the coordinates that you're feeding to namd, and check if that error appears again.

Regards,
Nuno
  ----- Original Message -----
  From: lily jin
  To: vmd-l_at_ks.uiuc.edu
  Sent: Wednesday, February 22, 2006 8:01 PM
  Subject: vmd-l: restart simulation with NAMD

  ``atoms moving too fast; simulation has become unstable''

  I am fine with a start-from-scratch run. But as I resume the simulation with restart conformation files, I got the error messege as above. Is there a problem with my original PDB or PSF file? Or there is something wrong with my previous simulation (There is no error message)?
  I changed the cutoff value and pairelistdist value, the problem is still there.
  Do you have any advice?Thanks!

  Lily

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