AMBER Archive (2004)

Subject: AMBER: Turning off non-bond interactions

Date: Wed Apr 21 2004 - 03:22:21 CDT

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.


Dave Evans
London School of Pharmacy

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