On 2011-03-16 16.35, Jesús Carrete Montaña wrote:
Dear list members,
I am running some simple simulations of pure ethanol and methanol using
the opls-aa force field as implemented in GROMACS 4.5.3, as a test case
before attempting to study mixtures with more complex molecules. My
problem is that, even though there are published results [1] that show
that this force field can yield satisfatory estimates of the density of
methanol, I am getting an average density around 745 kg/m3, much lower
than the expected 786 kg/m3.
Attached you can find all the relevant imput files (em.mdp is for the
initial energy minimization, stab.mdp for the "stabilization" run and
run.mdp for the "production" run; sample methanol.gro only contains one
molecule). I got good results for ethanol and ethanol/water mixtures using
basically the same set of mdp files, so I suspect the problem is in my
input .gro file, but I haven't been able to spot it. I would be thankful
for any help you could provide.
Best wishes,
Jesús
[1] G. Kaminski and W. L. Jorgensen, J. Phys. Chem. 1996, 100, 18010-18013.
Check Wensink et al. JCP 119 (2003) 7308. Did you turn on PME,
dispersion correction etc?
--
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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