[gmx-users] viscosity calculation_2

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 30 19:43:59 CEST 2010

On 2010-09-30 19.36, Payman Pirzadeh wrote:
> It does not explain for all files or all columns. For example, in the
> evisco.xvg, the following lines are written, but there are 5 columns (one of
> which is time). What are the rest? And the unit of the column (written
> below) is not clear to me.
> @    title "Shear viscosity using Einstein relation"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "(kg m\S-1\N s\S-1\N)"
> Same column are in the eviscoi.xvg (below).
> @    title "Shear viscosity integral"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "(kg m\S-1\N s\S-1\N ps)"
> I do not exactly know the relation between the two files and how I should
> use them. Also, the enecorr.xvg looks like to be a correlation function. But
> its unit is not clear and I do not know how to use it.
> I will be appreciated if you could clarify them.
> Regards,

I recommend that you read the paper by Hess (JCP 2002) about viscosity.
> Payman
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Dallas Warren
> Sent: September 29, 2010 7:11 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] viscosity calculation_2
> Sorry, haven't looked at these files before so this might not be the
> case, but doesn't the top of the .xvg file explain what each column is?
> Catch ya,
> Dr. Dallas Warren
> Medicinal Chemistry and Drug Action
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu
> +61 3 9909 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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