Visco.xvg and evisco.xvg

GROMACS version: 2021

Dear All,

I am computing viscosity using gmx energy. I observe that the shear viscosity in the visco.xvg file is different from that in the evisco.xvg file by a factor 4. What is the reason for this difference and which file should I refer to for shear viscosity?

In addition, for a simulation run of 200 ns, the data in the visco.xvg file is for 100 ns whereas data in the evisco.xvg file is for 50 ns. What would be the reason for this discrepancy?

Thank you.

Regards,
Kunal Mavani

I get comparable numbers.

How often do you write out your energies? For water I an output interval as small as 0.05 ps to get reasonable results due to the short correlation times.

The output is all integrals over correlation functions. These get more noisy as time progresses, so they are off, somewhat arbitrarily, all half and 1/4 of the analysis interval length.

Dear Hess,

Thank you for your response. I’m using MARTINI forcefield for which my time step is 20 fs and I write my energy every 10 timesteps, thus 200 ps. For a 200 ns run my visco.xvg has data for 100 ns whereas my evisco.xvg has data for 50 ns. Why is that discrepancy in the output file?

My viscosity from visco.xvg at 50 ns is 570 cP whereas at 100 ns it is 1143 cP (seems like a garbage value). Viscosity from evisco.xvg at 50 ns is 466 cP.

Last few data points from both the files are as below:

Output visco.xvg:
99997.8 1143.79 -221.001
99998 1143.78 -220.994
99998.2 1143.78 -220.988
99998.4 1143.77 -220.981
99998.6 1143.77 -220.976
99998.8 1143.77 -220.97
99999 1143.76 -220.964
99999.2 1143.76 -220.958
99999.4 1143.75 -220.954
99999.6 1143.75 -220.95
99999.8 1143.75 -220.944

Output from eviso.xvg:
49997.9 0.498095 0.0687884 0.833989 0.466958
49998.1 0.4981 0.0687521 0.833905 0.466919
49998.3 0.498067 0.0686986 0.833925 0.466897
49998.5 0.498068 0.0686559 0.833968 0.466897
49998.7 0.498059 0.0686198 0.833964 0.466881
49998.9 0.497993 0.0686087 0.833945 0.466849
49999.1 0.498003 0.0686044 0.833913 0.46684
49999.3 0.497983 0.068603 0.833868 0.466818
49999.5 0.497981 0.0685842 0.833973 0.466846
49999.7 0.497959 0.0685688 0.833944 0.466824
49999.9 0.497975 0.0685794 0.834015 0.466857
50000.1 0.497984 0.0686303 0.834007 0.466874

How should I correctly interpret the results?

Thank you.

Regards,
Kunal Mavani