On Tue, Dec 01, 2020, Franz Waibl wrote:
>
>It was my understanding that the internal energy contributions of the
>"vanishing" state (TI region 1) would automatically be kept regardless
>of lambda, since this is also done in the 1-step transform using
>Softcore potentials, and since it seems to be a reasonable thing to do.
The behavior you describe above is only activated when softcores are
requested. I'll let Darrin (or others more familiar with the current TI
codes in pmemd) answer the rest of the questions.
But the idea behind "softcore" is that you can have different numbers of
atoms in the two end-states. For example, lambda=0 could be ligand +
water, and lambda=1 could be water alone. Or, lambda=0 could be
compound1 + environment and lambda=1 could be compound2 + environment.
Without softcore, you must have the same number of atoms in the two end
states.
....dac
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Received on Tue Dec 01 2020 - 11:30:03 PST
