SMD atoms are not moving in accordance with steering parameters!

From: Gungor Ozer (
Date: Wed Jun 20 2007 - 22:35:59 CDT

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...


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