Viscosity calculation gmx energy

User discussions
1

GROMACS version: 2021
GROMACS modification: No

Dear All,

I am calculating viscosity using gmx energy -vis which uses Einstein’s relation. I’m running the simulation for 200 ns. I am interested in the output files visco.xvg and evisco.xvg.

  1. In the visco.xvg I see that I have data till 100 ns and for evisco.xvg till 50 ns. Why is that so and what is the difference? I expected both the files to have equal data points.
  2. The shear viscosity data in the visco.avg (54.8 cP) file differs significantly from the last column of the evisco.xvg (192 cP). Data from which file should be referred for shear viscosity?

Output from visco.xvg
Time (ps) Shear vis (cP) Bulk viscosity
99998 54.864 357.352
99998.2 54.8626 357.348
99998.4 54.861 357.344
99998.6 54.8591 357.34
99998.8 54.8571 357.338
99999 54.8552 357.335
99999.2 54.8537 357.331
99999.4 54.852 357.327
99999.6 54.8503 357.322
99999.8 54.8483 357.32

Output from evico.xvg
49998.5 0.184633 0.304404 0.0879212 0.192319
49998.7 0.18464 0.304396 0.0879256 0.192321
49998.9 0.184656 0.3044 0.0879333 0.19233
49999.1 0.184692 0.304371 0.0879252 0.192329
49999.3 0.18471 0.304369 0.0879221 0.192334
49999.5 0.184667 0.304372 0.0879115 0.192317
49999.7 0.184679 0.304385 0.0879139 0.192326
49999.9 0.184678 0.304385 0.0879119 0.192325
50000.1 0.184678 0.304362 0.087925 0.192321

Thank you very much.

Regards,
Kunal Mavani