AMBER Archive (2009)

Subject: Re: [AMBER] reaction coordinates

From: David A. Case (
Date: Wed Jan 14 2009 - 07:00:59 CST

On Wed, Jan 14, 2009, Rausch, Felix wrote:
> I would like to set up a MD simulation with reaction coordinates (distance
> between two atoms), but I'm not sure where I have to put the required
> parameters at in the input file. Unfortunately, the general descriptions in
> the manual don't help me out.

If you want to add a restraint based on such a distance, these would be
called "NMR" constraints in Amber-ese. Look at the examples in Section
6.11 of the Users' Manual, and in Tutorial A4..

Another possibility is ABMD, described in Section 4.6. See tutorial


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