[gmx-users] Re:Viscosity calculations
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 17 20:35:51 CET 2011
Please, in the future, do not reply to the entire digest. Cut out the relevant
portions. Otherwise, the archive gets very confusing.
Xiaohu Li wrote:
> Either of these are possible. Have you tried (1) different
> parameters or (2)
> longer simulations? If the model does not reproduce the experiment,
> it is not a
> very good model...
> What about those files evisco.xvg, eviscoi.xvg and visco.xvg? which one
> could be the correct file to look at?
Look into the source to see how each is calculated; evisco.xvg and eviscoi.xvg
are related to the Einstein relation (function einstein_visco in
src/tools/gmx_energy.c), presumably visco.xvg (function analyse_ener) is from
Green-Kubo, but do check yourself.
> I'm using OPLS-AA force field, the density and enthalpy of evaporation
> are both reasonably reproduced. However, kinetic studies using
> OPLS-AA on ionic liquid seems scarce(or I know little enough to not
> aware of what has been done).
Then you may want to do a bit more homework on your potential model. I don't do
ionic liquid simulations, but I certainly know there are plenty of published
papers out there.
> > Since it is not getting any useful result, I turned to
> > MD by applying a shear external force, which is in (2)
> > (2) I tried both NVT and NPT simulations which uses berendsen
> > bath. and set up the cos_acceleration = 0.1 nm/ps^2.
> > However, I tried to use g_energy -f *edr -s *tpr and by selecting
> > the 1/Viscosity or 2CosZ*Vel-X option, the output are giving me zero
> > data points on all times.
> This could be related to a bug that was fixed just a few days ago.
> Try pulling
> the latest stable release from git and trying again.
> That sounds like a solution, can you provide a link?
Pull the stable version.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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