AMBER Archive (2007)

Subject: Re: AMBER: getting same box dimension

From: David A. Case (case_at_scripps.edu)
Date: Mon Feb 26 2007 - 20:10:30 CST

On Mon, Feb 26, 2007, bertrand russell wrote:
>
> I am trying to run a simulation with a system which already has been
> equilibrated. In order to alter coordinates of a particular atom I created a
> .pdb file and altered the coordinates. Previously I equilibrated and ran a
> production run of around 5ns. Now I want to run leap to generate new .crd
> and .top files for the coordinate altered system to continue my run. How can
> I get the same box dimension of my previous run? Many thanks in advance.

In this situation, you should probably just hand-edit the restart file to
change the coordinates of the particular atom in question. Assuming that the
new energy is not enormously different than the old one, you would just
continue the run.

...good luck...dac
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