--- On Fri, 30/3/12, David van der Spoel <[email protected]> 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. Thanks, Ignacio -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
