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Xiaohu Li wrote:
<snip>
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
non-equilibrium
> MD by applying a shear external force, which is in (2)
> (2) I tried both NVT and NPT simulations which uses berendsen
coupling
> 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?
http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Novice
Pull the stable version.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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