[gmx-users] Re: Viscosity calculation using cos_acceleration
Dr. Vitaly Chaban
vvchaban at gmail.com
Tue Apr 16 09:36:49 CEST 2013
>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 <jamesresearching at 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
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