Re: AMBER: A question about Dynamics.

From: David A. Case <>
Date: Mon, 18 Sep 2006 13:55:47 -0700

On Mon, Sep 18, 2006, Qingning Shu wrote:

> I have a question about dynamics. I have a system. In Equilibration step I
> used cartesian restraint on the residues that are far away from active site.
> What shuold I do in the production MD, maintain the restraint or remove it?
> I thought I should keep it and ran the preoduction MD with the restraint.
> But I found in the potential-Vs-time plot the potential energy suddenly
> dropped at the beginning point of production MD. In other words, the
> potential energy was not continuous at that point.

Of course, the code itself has no idea what you mean by "equilibration" or
"production". So, if there is a sudden big drop in energy from one part of the
simulation to the next, something probably has changed. Your posting
indicates that the restraints did not change, so you need to look carefully
to see what *did* change. With a discontinous potential energy, it may be
that you didn't really start one part of the simulation from the end point of
the previous one. You should therefore double-check your file assignments and
so on.

...good luck...dac

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Received on Wed Sep 20 2006 - 06:07:12 PDT
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