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

[David van der Spoel]

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
> 
> 
> 
> 
> regards,
> Jes
> 
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se