[gmx-users] viscosity calculation using g_energy (3.3.3)

[Berk Hess]

Hi,

This is a very inefficient method for determining the viscosity.
Also you need really perfect pressure fluctuations: NVT, shifted potentials,
probably even double precision.
There was a mail about this recently.
There are better methods, have a look at:
http://dx.doi.org/10.1063/1.1421362

Berk


Date: Thu, 12 Mar 2009 07:39:52 +0000
From: jesbman at rediffmail.com
To: gmx-users at gromacs.org
Subject: Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)
CC: 


David,



Thanks for the quick reply.



Indeed I did  as what you suggested- g_energy -f water.edr -vis test.xvg 



The output file created includes three columns.



1. time ( ps) 2. shear viscosity (3) I assume it is bulk viscosity.



It seems, the unit given is cp. ( 1cp= 1* 10¯3 Pascal Second).



The bulk viscosity of water at 300 K is approximately 0.7 cp. But the value ( Bulk viscosity) I got from the program gives me 100 pa-s, an increase of two order of magnitude. I wonder whether I have done anything wrong while specifying the frequency of saving energy file.



I have saved the energy file in every 2ps. Isn´t that enough for a simple system like water? OR should I have to save trajectories in every 5fs as suggested by one in a previous post.



I post the first 20 lines of the output file.



-------------------------------------------------------------------



# This file was created Thu Mar 12 16:20:09 2009

# by the following command:

# g_energy -f water.edr -vis test.xvg 

#

# g_energy is part of G R O M A C S:

#

# GROup of MAchos and Cynical Suckers

#

@    title "Bulk Viscosity"

@    xaxis  label "Time (ps)"

@    yaxis  label "\8h\4 (cp)"

@TYPE xy

@ view 0.15, 0.15, 0.75, 0.85

@ legend on

@ legend box on

@ legend loctype view

@ legend 0.78, 0.8

@ legend length 2

@ s0 legend "Shear"

@ s1 legend "Bulk"

   1.99203      9.6633     96.3893

   3.98406     11.1625     98.1365

    5.9761     12.6631      99.838

   7.96813     13.4652     101.366

   9.96016     13.7012     100.249

-------------------------------------------------------------------------





regards,

Jes



On Thu, 12 Mar 2009 David van der Spoel wrote :

>JMandumpal wrote:

>>Dear GROMACS users,

>>

>>                           As explained in the manual ( page 139, section 6.5/3.3.3) I would like to calculate viscosity of my system ( water) using g_energy. I opted    (40  Mu-X ) from the g-energy selection. But the unit written on the Y axis of the corresponding xvg file is  (kJ mol\S-1\N). I think GROMACS uses SI unit , which is Pa-Second in the case of viscosity. Then why is this discrepancy.? Or did I make any mistake?

>>

>Mu is the dipole (in Debye). The units of these things are incorrect for everything that is not an energy. This will be fixed in the next gmx version. g_energy -h tells you what to do:

>

>g_energy -f ener -vis viscosity

>

>>

>>------I give the command on the prompt:

>>

>>g-energy -f ener.edr - o viscosity.xvg ;

>>then chose option 40 ( Mu-X).

>>

>>system details:

>>******************

>>My system consists of 500 TIP4P water molecules, ran for 3.5 nanoseconds at 150K, the ensemble is NPT. The version I am using is 3.3.3








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