AMBER Archive (2004)

Subject: Re: AMBER: add dummy atoms

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 23 2004 - 10:27:48 CST

On Tue, Nov 23, 2004, tang kwa wrote:
>
> I have use AMBER version 8 and I would like to do the
> umbrella sampling by using Sander. I will perform
> individual simulation by varing the distance between
> two residue.The distance should be between the center
> of the geometries.

You don't need (or want) any dummy atoms to do this. Set the value of IAT
to be negative, and use the IGR array to define the group of atoms whose
center of mass you want to refer to. See pp. 119-123 of the Users' manual.

I would also recommend (if you haven't done so already) that you experiment
a bit with simpler biassing potentials to see what kinds of output you should
expect, before trying the more complex cases.

...dac

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