<P>
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>
</P>
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