Re: [AMBER] Thermodynamic Integration

From: Ignacio J. General <>
Date: Thu, 17 Mar 2011 10:09:19 -0400

Thanks for your answer. So, in the charge part of TI all interactions are
reduced. But I don't understand what you say about the SC interactions. I
assume in the VDW part of TI you also tell amber to put all the VDW
parameters (corresponding to A) to zero, so that even internal interactions
(A-A) are reduced. Is this correct?



On Thu, Mar 17, 2011 at 5:10 AM, <> wrote:

> Hi,
> > 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,
> Thomas
> 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 - 07:30:04 PDT
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