[gmx-users] Density of methanol too low

David van der Spoel spoel at xray.bmc.uu.se
Wed Mar 16 16:39:29 CET 2011

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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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