On 2012-03-30 19:39, Ignacio Fernández Galván wrote:
--- On Fri, 30/3/12, David van der Spoel<sp...@xray.bmc.uu.se> wrote:
There are 459 solvent (acetonitrile) molecules. Not too
many, I know, but it's box size of ~40 Å.
And how are you treating the linear angle?
Nothing special. I built an OPLS-AA topology with 5 bonds, 7 angles, 3 dihedral and 3
pairs (<http://djelibeibi.unex.es/files/ACN.itp>). Visual inspection of the
conformations shows an almost linear CN group in every molecule, and g_angle gives an
average of 177, and a distribution that looks fine to me.
Is it starting from an equilibrated liquid?
Yes, or so I believe. I run a 50 ps equilibration
first, and use the resulting checkpoint with -t
Have you checked the diffusion constant to test whether it
is liquid?
You can do that from the VACF and from the mean square
displacement.
From g_msd I get a D of around 5.6e-5 cm^2/s which looks about the right order
of magnitude? (Default OPLS-AA acetonitrile is not very good, anyway.)
Integrating the VACF gives 4.8e-5 cm^2/s
Perhaps I should try with a larger system / longer simulation?
I can provide all the input files if needed.
No need, I think it is just fine!
What your seeing is the average vacf per atom, and apparently there are
correlations between the vibrations which cause the oscillation. In
theory both VACF should be the same but they are relatively close. A
longer simulation is always good of course.
Thanks,
Ignacio
--
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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