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 - 06:00:02 PDT
