From: Peter Freddolino (petefred_at_ks.uiuc.edu)
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?
Peter
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...
>
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