I use the SD integrator with tau_t = 1.0 ps for all of my work, including proteins in aqueous solution or embedded in a lipid membrane.
Any value of tau-t is "correct", and none will give you the proper dynamics, but I find that the diffusion of both water and lipids is quite reasonable when using tau_t=1.0 ps. I arrived at 1.0 ps after some help from Berk Hess on this list. I suggest that you search out those old posts. Chris. -- original message -- In manual I've found possibility of the usage of the sd (langeven's dynamics) integrator as the thermostat. It's known that friction coefficient in the Langeven's equations is defined as m/Tau_t. So the high values of tau t can be appropriate for the modeling of the thermostat without t_coupl. Also I know that friction coefficient for such simulation must corresponds to the viscosity of the system. In Gromacs manual I've found that Tau-t= 2.0 ps can be appropriate value for such simulations. Does this value suitable for water-soluble system only ? What Tau_t should I use for modeling of the membrane proteins in the lipid-water environment which has higher viscosity ? Thanks for help, James -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
