Re: [AMBER] co-alchemical ion

From: accuratefreeenergy--- via AMBER <amber.ambermd.org>
Date: Mon, 24 Oct 2022 17:32:45 -0400

Hi Pietro,

        It would be easier for us to figure out if you can give us the input files that can reproduce the issues. Thanks!

Best,

Taisung

-----Original Message-----
From: David A Case via AMBER <amber.ambermd.org>
Sent: Monday, October 24, 2022 8:32 AM
To: Pietro Vidossich <Pietro.Vidossich.iit.it>; AMBER Mailing List <amber.ambermd.org>
Cc: Taisung Lee <taisung.gmail.com>; Darrin York <Darrin.York.rutgers.edu>
Subject: Re: [AMBER] co-alchemical ion

On Sun, Oct 23, 2022, Pietro Vidossich via AMBER wrote:
>
>we are facing unstable simulations while trying to alchemically
>transform a neutral peptide into a (negatively) charged one, coupled to
>the transformation of an ion (chloride) into a water molecule (the
>co-alchemical ion approach from the literature). The simulation shows
>huge spikes in temperature and in the forces acting on chloride and the
>coupled water molecule, eventually resulting in out of scale energy
>components (e.g. EPtot = **************). What is puzzling us is that
>the problem shows up only when the two transformations are simultaneously performed:
>independent simulations (one to transform the peptide and another to
>transform the ion) complete with no issues.

I'm no expert here, and have never tried this sort of calculation. But I'm wondering if there is something in the TI code that breaks if the two regions that are changing (in your case peptide + ion/water) are far apart:
basically, the "TI region" (the union of these two) becomes very large.

I'm cc-ing this to some free energy experts who only rarely follow this list.

....dac


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Received on Mon Oct 24 2022 - 15:00:05 PDT
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