[gmx-users] Re:Viscosity calculations

[Justin A. Lemkul]

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:

<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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