[gmx-users] On the usage of SD integrator as the thermostat
Christopher Neale
chris.neale at mail.utoronto.ca
Fri Nov 23 17:43:49 CET 2012
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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