AMBER Archive (2006)

Subject: Re: AMBER: A question about Dynamics.

From: Chunhu Tan (tanc_at_uci.edu)
Date: Mon Sep 18 2006 - 16:24:22 CDT

Just a guess ... If you did a NPT simulation and used the same structure
as the reference, sometimes the restarted potential energy had a sudden
drop if the simulation did not stopped with Vlimit error.

-----邮件原件-----
发件人: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] 代表
David A. Case
发送时间: Monday, September 18, 2006 1:56 PM
收件人: amber_at_scripps.edu
主题: Re: AMBER: A question about Dynamics.

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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