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: jesb...@rediffmail.com
To: gmx-users@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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