[AMBER] PMEMD and Steered MD

From: Ali M. Naserian-Nik <naseriannik.gmail.com>
Date: Mon, 17 Sep 2012 14:12:51 +0430

Hi all,

I m trying to do some steered MD simulations with pmemd 12 in which the
distance between two atoms must be increased while the angle made between
three atoms must be fixed at its initial value. I know that it is
performable easily by using jar and ncsu_pmd by sander. However, it seems
that ncsu is not accessible in pmemd, and on the other hand if two
restraints is added in the restraint file for steered MD (one for
increasing the distance and another for keeping the angle constant), only
the first restraint in the restraint file would be applied and the other
would be ignored by the code. Is there a way to perform this kind of
simulations through pmemd 12? I'd be so grateful if anyone could help me on
these issues.

Kind regards,

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Received on Mon Sep 17 2012 - 03:00:04 PDT
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