[gmx-users] On the usage of SD integrator as the thermostat

[Krzysztof Murzyn]

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.neale at 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
> --
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