I am wondering what you mean by 'proper dynamics', Chris? And in general, what's the advantage of using sd integrator over md integrator together with Nose-Hoover thermostat.
Thanks, km. On Fri, Nov 23, 2012 at 5:43 PM, Christopher Neale <chris.ne...@mail.utoronto.ca> wrote: > 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 -- 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