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 <hyunj...@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. > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.