Re: SMD atoms are not moving in accordance with steering parameters!

From: Peter Freddolino (
Date: Thu Jun 21 2007 - 08:51:14 CDT

Hi Gungor,
could you please elaborate on this behavior a bit? How exactly did the
pulled residue move? How long was your simulation? And did the SMD lines
of the log file indicate pulling in the appropriate direction?

Gungor Ozer wrote:
> Hello all,
> I have been trying to run a Steered MD simulation on a small peptide.
> What I've been doing is basically pulling a whole residue at a
> realtively appropriate velocity (10^-4 orders of magnitude of
> A/timestep) in a box full of TIP3 water molecules at 500K. The
> aminoacid is not a part of a beta strand or an alpha helix and its
> only non-bonded interactions are those with waters.
> The problem I am facing is simply that my steered residue was not
> moving along the direction vector and velocity I have been assigning.
> Does anybody know what I might be doing wrong? Or, has anybody
> experienced similar problems? And finally, do you have any potential
> explanation (or solution) to this issue?
> Thank you all in advance...

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:52 CST