From: "David Mobley" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[email protected]>
To: "Discussion list for GROMACS users" <[email protected]>
Subject: Re: [gmx-users] Re: WCA and free energy calculations
Date: Mon, 25 Jun 2007 09:32:05 -0700
Berk,
Nearly anything can be done now in Gromacs :) (although sometimes not
easily).
Maybe I missed something, but according to me it should work.
Tabulated potentials work just like any other potential.
So they are soft-cored when the LJ-parameters or charge of one of
the two atoms in the pair interaction is different in state A and B.
So if you have the WCA potential set up propely (maybe using
energygrp-tables
if you want different sigma's), then the free-energy part is trivial.
OK, so you're saying that the radii used when looking up interactions
in the interaction table are the "effective radii" including the soft
core modifications? (If not, how can one specify different potentials
to use depending on whether the particle is soft core or not?)
If it's the effective radius -- can I suggest this be documented in the
manual?
Thanks for the help. I'd love to be able to do these (have a huge
project planned where this would be immensely useful).
This issue is a bit confusing, I'll try to explain it in more detail.
To use WCA in Gromacs, you need to have a different table
for every sigma_ij that occurs between atom pairs, since the LJ
tables can not cut-off the interactionss exactly at the WCA cut-off.
So you can fill either the dispersion or the repsulsion table with
a WCA potential with a given sigma. The appriopriate C6 or C12
value with then scale this potential.
To avoid confusion I would use C6/C12 input, not sigma/epsilon,
since only one of the two LJ tables is used.
To have different sigma_ij's in one simulation, you need to use
the energygrp_table mdp option.
For doing free-energy calculations with such a system you need
to set C6 and C12 appropriately.
Say you have filled the dispersion table with WCA, the repulsion
table should then be zero. You can then set C6 in the A and B
state differently as needed. To have the proper soft-coring
you will then need to set C12 such that sigma=(C12/C6)^1/6
matches the sigma of the WCA potential in your table.
It would of course be nicer to have full WCA support in the innerloops,
but that would again give many more loops...
Currently I would assume WCA is not used much,
although our group could use it for coarse-grained simulations.
Berk.
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