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Hi,<br><br>This is a very inefficient method for determining the viscosity.<br>Also you need really perfect pressure fluctuations: NVT, shifted potentials,<br>probably even double precision.<br>There was a mail about this recently.<br>There are better methods, have a look at:<br>http://dx.doi.org/10.1063/1.1421362<br><br>Berk<br><br><br><hr id="stopSpelling">Date: Thu, 12 Mar 2009 07:39:52 +0000<br>From: jesbman@rediffmail.com<br>To: gmx-users@gromacs.org<br>Subject: Re: Re: [gmx-users] viscosity calculation using g_energy (3.3.3)<br>CC: <br><br>
David,<br>
<br>
Thanks for the quick reply.<br>
<br>
Indeed I did as what you suggested- g_energy -f water.edr -vis test.xvg <br>
<br>
The output file created includes three columns.<br>
<br>
1. time ( ps) 2. shear viscosity (3) I assume it is bulk viscosity.<br>
<br>
It seems, the unit given is cp. ( 1cp= 1* 10Ŋ3 Pascal Second).<br>
<br>
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.<br>
<br>
I have saved the energy file in every 2ps. Isnīt 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.<br>
<br>
I post the first 20 lines of the output file.<br>
<br>
-------------------------------------------------------------------<br>
<br>
# This file was created Thu Mar 12 16:20:09 2009<br>
# by the following command:<br>
# g_energy -f water.edr -vis test.xvg <br>
#<br>
# g_energy is part of G R O M A C S:<br>
#<br>
# GROup of MAchos and Cynical Suckers<br>
#<br>
@ title "Bulk Viscosity"<br>
@ xaxis label "Time (ps)"<br>
@ yaxis label "\8h\4 (cp)"<br>
@TYPE xy<br>
@ view 0.15, 0.15, 0.75, 0.85<br>
@ legend on<br>
@ legend box on<br>
@ legend loctype view<br>
@ legend 0.78, 0.8<br>
@ legend length 2<br>
@ s0 legend "Shear"<br>
@ s1 legend "Bulk"<br>
1.99203 9.6633 96.3893<br>
3.98406 11.1625 98.1365<br>
5.9761 12.6631 99.838<br>
7.96813 13.4652 101.366<br>
9.96016 13.7012 100.249<br>
-------------------------------------------------------------------------<br>
<br>
<br>
regards,<br>
Jes<br>
<br>
On Thu, 12 Mar 2009 David van der Spoel wrote :<br>
>JMandumpal wrote:<br>
>>Dear GROMACS users,<br>
>><br>
>> 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?<br>
>><br>
>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:<br>
><br>
>g_energy -f ener -vis viscosity<br>
><br>
>><br>
>>------I give the command on the prompt:<br>
>><br>
>>g-energy -f ener.edr - o viscosity.xvg ;<br>
>>then chose option 40 ( Mu-X).<br>
>><br>
>>system details:<br>
>>******************<br>
>>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<br>
<BR>
<br><br>
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