Hello, I would like to calculate bulk and shear viscosity on gromacs using g_energy. I have read a number of other emails about this topic but there still seems to be no conclusive answer to how to use this tool. I use the following command:
gmx energy -f prod_500.edr -vis viscosity.xvg >From this, a file called 'viscosity.xvg' is produced with data on time (ps), shear viscosity, and bulk viscosity. However, these values fluctuate wildly and are off from the correct viscosity for this model (SPCE) by at least an order of magnitude. I know the simulation trajectory is correct as I have matched potential energy, density, and diffusion coefficition for these runs with literature. However, the viscosity numbers are far off from the expected values. Any suggesions on what I can try? I assume there must be a way to do it by hand via the pressure tensors. Can someone directly me to how I can practically take the pressure tensors to calculate via Green-Kubo method the viscosity? Thanks, Shuwen -- 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.
