[gmx-users] Viscosity using periodic perturbation method

[Yanmei Song]

Dear Herk:

Thank you so much for your help!

Maybe the way I asked make it confusing. I read your paper: " Determing the
shear viscosity of model liquids from molecular dynamics simulations"  You
used NVT. My question is which one is better? NPT or NVT? Or you can use
either of them.

"Strictly speaking it might be incorrect, but since pressure scaling is
usually less than 1%
it will not affect your results significantly."

So technically we should use NVT for the periodic perturbation method,
right? Thanks!

On Tue, May 26, 2009 at 12:03 AM, Berk Hess <gmx3 at hotmail.com> wrote:

>  Hi,
>
> Yes, you can use NPT, the code takes care of this properly.
> Strictly speaking it might be incorrect, but since pressure scaling is
> usually less than 1%
> it will not affect your results significantly.
>
> Berk.
>
> ------------------------------
> Date: Mon, 25 May 2009 15:19:10 -0700
> From: ysong30 at asu.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Viscosity using periodic perturbation method
>
>
> Dear users:
>
> I was trying to calculate the viscosity of liquid system using periodic
> perturbation method. Does this method require NVT ensemble simulation in
> stead of NPT ? Because I read some literature on periodic perturbation
> method. they all used NVT.  I did not found any information about this on
> the manual. Can I use NPT Non-equilibrium MD in order to use periodic
> perturbation method? Thanks in advance!
> --
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
>
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-- 
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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