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?
Best,
Dan
On Fri, Oct 6, 2017 at 11:05 AM, Khabiri, Morteza <khabiri.med.umich.edu>
wrote:
> 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
