Re: [AMBER] Thermodynamic integration/switch off/on cloumbic and vdw interactions

From: Daniel Mermelstein <>
Date: Mon, 9 Oct 2017 10:40:02 -0700

Hi Morteza,

coulombic: you can use crgmask to zero the charges on atoms whose coulombic
potential you don't want to count.

vdw: I don't know of a simple way using TI. You might be able to substitute
in zeroes for the vdw terms you don't want to count, but I've never tried
doing that.

bonded: maybe. This depends on what you mean exactly by switching the
bonded terms off. What transformation are you trying, exactly?



On Fri, Oct 6, 2017 at 11:05 AM, Khabiri, Morteza <>

> Hi all,
> I am currently using pmemd for ti calculation. I would like to dissect the
> vdw and coulombic interactions during transition process. I would like to
> kno, is it possible to perform an alchemical transition in Amber by
> switching on/off bonded, vdw and coulombic interactions separately?
> Thanks
> Morteza
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Daniel J. Mermelstein, Ph.D candidate
McCammon & Walker Groups
Department of Chemistry & Biochemistry
University of California, San Diego
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Received on Mon Oct 09 2017 - 11:00:02 PDT
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