Re: [AMBER] Adaptively Biased Molecular Dynamics

From: case <>
Date: Tue, 6 Dec 2011 20:51:42 -0500

On Tue, Dec 06, 2011, Aron Broom wrote:
> 2) I ran the water dimer test just using the oxygens for each water and the
> PMF is semi-reasonable, but the entire simulation suffers from the fact
> that the distance can become larger than the range I'm interested in.

You could use a "flat bottom" NMR-type constraint to keep the O=O distance
from getting too big, e.g.

  &rst iat = 3,6, r1=0.1, r2=2.0, r3=12.0, r4=99.0, rk2 = 0.0, rk3=10.0, /

This (untested!) restraint will have no effect until the distance between
atoms 3 and 6 gets to 12 Ang, and then the energy will rise quickly, pushing
the two molecules back together.


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Received on Tue Dec 06 2011 - 18:00:03 PST
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