[gmx-users] about cos-accelation

Dr. Vitaly Chaban vvchaban at gmail.com
Wed Jul 23 11:50:31 CEST 2014

1) g_energy -vis is always Einstein

g_energy and then select 1/visc term - NE method.

2) I do not think it makes physical sense to distinguish between
viscosities in a mixture because of the definition of viscosity.
Specifying cos-acc will supply extra energy to all particles.

3) Rigorously, one must use a set of values and extrapolate
viscosities to zero-acceleration. Some cunning researchers use a
single small value, though, and say that the uncertainty coming from
extrapolation is within viscosity error bars.

0.05 is a reasonable acceleration to start with, but it depends on the
simulated system.

4) The bug with volume was in the earlier 4th versions. I believe that
it was fixed around ver. 4.5.

Good luck.

Dr. Vitaly V. Chaban

On Wed, Jul 23, 2014 at 5:18 AM, Hyunjin Kim <hyunjink at andrew.cmu.edu> wrote:
> Dear,
> 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
> correct?
> Hopefully, my questions are clear. Thanks a lot for your support in advance.
> --
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