Xiaohu Li wrote:
Hi,
I'm trying to calculate viscosities of a few ionic liquid and has
roughly read about Hess's paper JCP 116 209, 2002.
Follows are the questions that I have
(1) For the method which uses the fluctuations of the pressure tensor
using Green-Kubo relation. I used g_energy -f *.edr -s *.tpr -vis option
and has obtained
a few files such as evisco.xvg, eviscoi.xvg and visco.xvg
The evisco.xvg seems like the one I'm interested, since it has the title as
@ title "Shear viscosity using Einstein relation"
and the unit seems also correct. This file has 5 columns, if I
understand it correctly(by extrapolating from Hess's paper), the second
to fourth columns are the results from the off-diagonal elements of the
pressure
tensor and the fifth one being the average. Hess's paper seems to be
this one(Figure 5). However, the results are way to low for the ionic
liquid, since I'm getting 1e-7 kg/m.s and way too low for a ionic liquid.
the eviscoi.xvg file seems to be some kind of integral of evisco.xvg
which I'm not quite getting what it is.
visco.xvg contains the shear viscosity and bulk viscosity, which again
seems to be the one I'm looking for. However, the shear viscosity I'm
looking is(the region which roughly is constant) about 3~5 times higher
than the experiment. The simulation is 12ns long. Of course, this could
mean (1) the force field is bad or (2) the Green-kudo converges too
slowly as Hess pointed out.
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...
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.
-Justin
I tried really hard on searching results on the user list of gromacs
but it seems that there are quite a lot questions on this but not a
single satisfactory answer has been given, the most popular answer
people gave is refer to Hess's paper, but even though Hess was giving a
good theoretical background on this paper, practically on how to set up
MD jobs is not given.
So I would appreciate anyone's hint.
Cheers,
Xiaohu
--
========================================
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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