Re: [AMBER] TI calculation steps

From: Song, Lin <>
Date: Thu, 5 Dec 2019 21:25:39 +0000


If you’re disappearing a molecule in one step, the initial state should be the molecule with full vdW and full charge, the end state should be nothing. So the mask should be : timask1=“molecule”, scmask1=“molecule”, timask2-=“”, scmask2=“”. No crgmask should be used.


> On Dec 5, 2019, at 3:24 PM, Debarati DasGupta <> wrote:
> Hi,
> Page 427 of the Amber18 manual says -----> Alternatively to the two-step process of removing charges from atoms first and then changing the vdW parameters of chargeless atoms in a second TI calculation, sander and pmemd also have a soft core version of the Coulomb equation implemented for single step transformations under periodic boundary conditions. This is automatically applied to all atoms in scmask…”
> If one does single step transformation, will the crgmask flag need to be applied?
> For absolute free energy calculations, disappear molecule….
> My timask2=’’, my scmask2=’’, but I am not sure of the crgmask…
> I have scalpha and a scbeta parameter according to equation 21.7 of the manual, but I am not sure of the usage of crgmask.
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Received on Thu Dec 05 2019 - 13:30:02 PST
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