Re: [AMBER] Thermodynamic Integration

From: <>
Date: Thu, 17 Mar 2011 05:10:20 -0400 (EDT)


> I do a TI with crgmask=':A', then the charges of A are going to be
> reduced.
> But are they going to be reduced also for internal interactions in A? In
> other words, interactions A-W are going to be reduced, but will
> interactions
> A-A (electrostatic) also going to be reduced?

In short: yes. crgmask is not directly connected to the TI algorithms, all
it effectively does is tell sander to read a prmtop *as if* some charges
were zero. Note that the opposite is true for single-step TI. There a
distinction between SC and non-SC interactions, which are softenend, and
SC-SC interaction, which are not changed, is made.

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Thu Mar 17 2011 - 02:30:03 PDT
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