The program will recognize the end state as nothing as you specified timask2=“” and scmask=“”. Nothing means no vdW and no charge. So it starts with full vdW and full charge, ends with no vdW and no charge.
Best,
Lin
On Dec 5, 2019, at 4:39 PM, Debarati DasGupta <debarati_dasgupta.hotmail.com<mailto:debarati_dasgupta.hotmail.com>> wrote:
So for my individual lambdas for equlibriation and production, I will not be using the “crgmask” flag. But how will the program understand that I am trying to remove all partial charges (de couple the ligand from the environment) from my ligand molecule?
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Subject: Re: [AMBER] TI calculation steps
Hi,
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.
Best,
Lin
On Dec 5, 2019, at 3:24 PM, Debarati DasGupta <debarati_dasgupta.hotmail.com<mailto:debarati_dasgupta.hotmail.com>> 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 - 14:00:02 PST
