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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