On 17/07/15 17:55, Justin Lemkul wrote:
On 7/17/15 11:29 AM, Daniele Veclani wrote:
I'm using gromacs version 5.0.4, so should I upgrade to version 5.0.5 ?
If you need [ pairs_nb ], yes. But I actually don't think you do. See
below.
I read in the manual (section 5.3.4) that can turn off the 1-4
interactions
without ever touching the topology, by using the couple-moltype,
couple-lambda0, couple-lambda 1, and couple-intramol keywords.
I think you're reading this section backwards. Admittedly, it's a
confusing section, so let's simplify.
If you turn off the nonbonded interactions of some molecule in water,
the total contribution to the free energy change is composed of the
solute-solute terms and solute-water terms. To get the actual solvation
free energy, one needs to correct for the solute-solute terms being
turned off, which is the purpose of the gas-phase simulations. Turning
off interactions in vacuo tells you how much of the free energy change
is attributed to intramolecular terms. The difference between the two
transformations is then the solvation free energy.
But, several years ago, this procedure became much easier in GROMACS
with the introduction of the "couple-intramol" keyword. It *eliminates*
the need for any gas-phase simulations or topology hacking. This is
what the manual is trying to tell you. If you run your transformations
in water with "couple-intramol = no," then the intramolecular
interactions are always full strength, so the free energy difference you
calculate is solely attributed to solute-water interactions, viz. the
solvation free energy.
If you *want* to make your life more difficult, set "couple-intramol =
yes" and conduct gas-phase calculations, as well, which is what requires
topology hacking. I wouldn't do this. Not only is the manual somewhat
unclear, but any time you have to manually modify the topology, there is
a potential for error. The free energy code attempts to make your life
easy and efficient, unless you have some very complex protocol to do
that requires lots of work. A solvation energy is not one of these
cases; it is straightforward with appropriate use of the .mdp keywords.
If I understand that correctly then the protocol ignores the difference
in intramolecular energy between gas-phase and solvation. This is
probably OK for small and rigid molecules but not necessarily for larger
or flexible molecules. When using polarizable force fields it will
probably induce a significant error. Have you tried this yet?
-Justin
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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