>Alternatively, has anyone else reproduced the viscosity calculation, or
> tried to? > If anyone would be so kind as to forward their input files, that might help > me narrow down the problem with my own input files. > > Thank you. > > James > > On 11 April 2013 16:55, James Cannon <jamesresearch...@gmail.com> wrote: > > > Dear Gromacs users, > > > > This question seems to come up periodically in the mailing list, but none > > of the previous answers seem helpful in my case. > > > > I'm trying to reproduce the viscosity calculation of SPC water by Berk > > Hess (JCP 116, 2002) using cos_acceleration in Gromacs. The answer I get > is > > 2 orders of magnitude out. > > > > My topology file and parameter file is appended at the bottom of this > > email. > > > > I run g_energy and get > > > > Energy Average Err.Est. RMSD Tot-Drift > > > > > ------------------------------------------------------------------------------- > > 1/Viscosity 23.4689 0.13 2.39126 -0.255371 (m > > s/kg) > > > > which gives a viscosity of 0.04 kg/(m s), or 40 mPa.s > > > > The value quoted in the paper is about 0.4 mPa.s which is around the > > correct value for water, give or take a bit. > > > > So my question is, where is my missing factor of 100? > Non-equilibrium method for viscosity heavily depends on the acceleration value. Your selection looks reasonable for me, but try to decrease the value. "Ideal" acceleration depends on the particular collective dynamics in each system, of course. I can soothe you ability a workability of the utility. It has been tried many times and works really perfectly. Dr. Vitaly Chaban -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
