GROMACS version: 2019.4
GROMACS modification: Yes
I am trying to calculate the viscosity of mixing system with CO2 and some molecular at various Tempaeratures and Pressures.
First, I tested the water box, and the result seemed to be acceptable.
Then I changed to CO2 system, even only CO2, the the value of 1/viscosity obtained by g_energy was not a bit correct. it fluctuated considerably from 1E+04 to 1.5E+05. I tested the cos_acceleration from 0.001 to 0.025, but somtimes it shown: “srun: error: nid00114: task 0: Segmentation fault
srun: Terminating job step 14252474.1”.
Could anbody help me to give some advice to calculate viscosity, pls? I appreciate it very much.
As you observed, the viscosity calculation with gmx energy converges very slowly and is very sensitive to the parameters you set, so using the cos_acceleration is definitely the way to go.
The segmentation fault indicates that the forces / velocities during your simulation are too high, so there are a few things you could try (if you didn’t already)
- use a different thermostat
v-rescale with a very low
- use a larger simulation system
- use a well-equilibrated initial structure, making sure that the system density is correct by running some NPT equilibration beforehand
In case you did not already find, see also
and the originial paper on which the method is based
Thanks so much. You helped me definitely and I ll try all your tips.