[gmx-users] about cos-accelation

Hyunjin Kim hyunjink at andrew.cmu.edu
Wed Jul 23 05:18:42 CEST 2014


As I understand, in order to calculate viscosity in Gromacs, I can use
"g_energy -f -vis ..." using .edr file after simulation.

Regarding this, I have four questions :

1. Regardless of including cos-acceleration command in my .mdp file,
I can obtain viscosity. This means that if I include cos-acceleration
during simulation, then the viscosity value is obtained from acceleration
(or non-eq method). Otherwise, the value is calculated using Einstein
relation. Am I right? Or will "g_energy -vis" always yields viscosity
using Einstein relation.

2. If I use mixture of molecules in the system, then can I calculate
viscosity for each molecule in the system?

3. I have checked mailing list, it looks people use different
cos-acceleration values, e.g., 0.1, 0.25, or 0.5 nm/ps^2. I wonder how
people choose the values? Does viscosity depend on this value?

4. If I use Gromacs 4.6.1 or higher, then is the bug for volume division

Hopefully, my questions are clear. Thanks a lot for your support in advance.

More information about the gromacs.org_gmx-users mailing list