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

JMandumpal jesbman at rediffmail.com
Thu Mar 12 08:39:52 CET 2009


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


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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