[gmx-users] soft-core and coulomb transformation

David Mobley dmobley at gmail.com
Mon Nov 5 15:18:51 CET 2007


> 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).

I am not sure what you mean by "directions". Can you clarify your
protocol? For example, the protocol used in my tutorial has no
directionality. The only way I can think of you having directionality
is if you are either:
(a) Using "slow growth" where lambda is a function of time
(b) Running your simulations consecutively, where the simulation at
each lambda value begins from the endpoint of the simulation at the
previous lambda value.

Neither of those is what I would particularly recommend, since both
introduce additional hysteresis. I'd instead recommend running
independent equilibrium simulations at different lambda values, making
sure you equilibrate long enough at each.

> 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?

To clarify, you want to NOT use soft core potentials for
electrostatics, and use SC for the LJ transformation.

You need to provide more detail on your protocol.


> i tried this for simple ala->gly and ethane->methane transformations.
> please give me some insight into the problem...
> bharat
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