Re: AMBER: Turning off non-bond interactions

From: David A. Case <>
Date: Wed, 21 Apr 2004 08:54:54 -0700

On Wed, Apr 21, 2004, wrote:
> I am trying to run an MD simulation where the non-bonded interactions of a
> small group of atoms are set to zero...
> The system however gives NaN halfway through an MD simulation when two atoms
> come close to each other.

I don't think you can avoid this without changing the code. Amber still
computes r**-12 for every pair of atoms, then multiplies by the appropriate
LJ parameters. What is probably required is to test _first_ for zero
parameters, and skip the calculation if appropriate. Another approach would
be to hack the excluded atom list, so that the dummy atoms were excluded from
all other atoms. Yet another idea would be to actually remove the atoms, and
add an artificial bond or NMR-like restraint to "tether" the parts of the
molecule together.

....good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Wed Apr 21 2004 - 17:53:00 PDT
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