[gmx-users] Re: Re: Is vacuum simulation NVT?

Michael Shirts mrshirts at gmail.com
Sun Dec 16 15:26:19 CET 2012

> 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.

More information about the gromacs.org_gmx-users mailing list