AMBER: Turning off non-bond interactions

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Date: Wed, 21 Apr 2004 09:22:21 +0100

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Dear Amber users,

I am trying to run an MD simulation where the non-bonded interactions of a=
 small group of atoms are set to zero, to investigate the steric effect of=
 this group. (I can't just cut it off as it's required to tether two other=
 bits of the molecule together.) I did this by creating new atom types with=
 identical bonding parameters to the atoms they were replacing, but with=
 VDW parameters 0.00 0.00, and setting the charges to zero also.

The system minimised fine, giving sensible geometry and energies compared=
 to the original system, which also runs unproblematically. The system=
 however gives NaN halfway through an MD simulation when two atoms come=
 close to each other. Physically, I can't see any reason why the atoms=
 shouldn't be able to pass through each other, but possibly there is some=
 place in the code where 1/0 is evaluated, or some other reason.

So, is it possible to somehow turn off the VDW/electrostatic evalutions for=
 particular atoms or pairs of atoms entirely, without running the risk of=
 this behaviour? If anyone has done this sort of thing before and can=
 suggest a good approach that would be very useful.=20


Dave Evans
London School of Pharmacy
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Received on Wed Apr 21 2004 - 09:53:19 PDT
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