Hello,
I have just read an interesting paper suggesting that the reference state in
free energy decoupling/coupling simulations should be the one with larger
entropy. Lu and Kofke "Accuracy of free-energy perturbation calculations in
molecular simulation. I. Modeling" JCP V. 114, N. 17 pp. 7303-7311 (2001).
I have seen some mention that:
<begin quote>
Ordinarily, one would expect that "forward" and "reverse" only are
meaningful when you're (a) doing nonequilibrium simulations, or (b)
beginning simulations at lambda values from the ending configurations
at preceding lambda values.
<end quote>
http://www.gromacs.org/pipermail/gmx-users/2008-February/032430.html
And now I am confused, since I would have thought that this was an important
"forward" vs. "reverse" difference, although I may have my terminology
wrong here.
To put my questions succinctly:
1. In the gromacs implementation, is there any important difference
between coupling and decoupling? I avoid the terms "forwrad" and
"reverse" in order to avoid non-equilibrium or slow-growth connotations.
2. Does soft-core work properly for both LJ coupling and LJ decoupling?
I am not clear how mdrun knows whether to soft-core lambda or 1-lambda
since it is near the decoupled state that really needs the soft-core,
and this could be at lambda or 1-lambda.
Background information:
I am doing coulomb and LJ separately; LJ only with soft-core; coulomb
first in the decoupling. Everything is working fine for me in the
decoupling department, but I am now considering switching to coupling
as opposed to decoupling based on this Lu 2001 paper and am interested
if anybody has some comments.
Thank you,
Chris.
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