AMBER Archive (2009)

Subject: [AMBER] Partial interactions

From: Ignacio J. General (
Date: Mon Apr 20 2009 - 16:07:24 CDT

Dear Amber users:

Is it possible to make some molecules of a system interact with only a
selected part of the rest, but not with everything else? To be more precise,
let's say I have a system with three types of molecules: A, B and C; can I
do a regular MD but where molecules A only interact with molecules B, not
with C (A doesn't see C and viceversa)?

Ultimately, I would like to do this in a thermodynamic integration, so that
the initial system, V0, is the regular three component system, and the final
system, V1, is the unphysical three component system where interactions A-C
are not computed.

Thanks for your help,

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