Dear all,
i am trying some very basic transformations by thermodynamic integration
to calculate free energy difference. By following mailing-list archive, i
learned that it is efficient to do coulomb transformations and LJ
transformations separately. i use David Mobley's tutorial values for
soft-coring, i.e., sc-alpha=0.5, sc-power=1, sc-sigma=0.3. As per list,
since charge transformations are not "hard", we are at liberty to use
soft-core potentials for coulombs and that is quite logical, and yes,
without sc, there is no problem in coulomb transformation.
Everything goes fine till this point. Now, i do reverse transformations to
check for hysteresis. For vdw transformations, i get almost perfect
overlap of dG/dlambda vs lambda for forward and reverse transformations,
but for coloumb transformations, if i don't use soft-core potentials, i
don't get any overlap (i understand that getting overlap in forward and
reverse transformations is not the accurate-enough measure of absence of
hysteresis, but for smaller systems 5 ns at each lambda value should be
sufficiently enough sampling).
Ny doubt is why should this happen? if there is no problem like
singularities in potentials, why should not using sc-potentials make
such a difference?
i tried this for simple ala->gly and ethane->methane transformations.
please give me some insight into the problem...
bharat
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