> Could you tell me is there any difference of different Tau_t ussage ( > inverse friction in case of Stochastic dynamics) for simulation of > water-soluble as well as membrane-proteins ? In the first case I'm > using tau_t 2ps that is lower than internal water friction. In the > second case one part of protein could be in the membrane ( e.g > helixes) but other ( e.g loops) in water media. Both of that solvents > have different characteristic viscousity. So what Tau_t should be used > in stochastic dynamics for such biphastic systems?
I don't think there is a "right" sd tau_t. You probably want at tau_t^-1 that is lower (tau_t longer) than the natural viscosity of either system, such that the viscosity of the actual intermolecular interactions dominates, not the unphysical viscosity of the thermostat. I don't know how much lower is good enough, though. You may have to experiment. -- 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
