[AMBER] TI calculation steps

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Thu, 5 Dec 2019 20:24:56 +0000


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 - 12:30:01 PST
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