[gmx-users] tau_t and tc_grps for v-rescale (2)
jalemkul at vt.edu
Fri Sep 28 12:45:56 CEST 2012
On 9/28/12 3:18 AM, Felipe Pineda, PhD wrote:
> Hi again,
> I posted yesterday the query below, but have not received any feedback up to
> now. I would like to put my question in another way: in Justin's "CAP-15 in
> DPPC" tutorial he uses during NVT equilibration Bussi's thermostat (V-rescale)
> together with three separate coupling groups:
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein DPPC SOL_CL ; three coupling groups - more accurate
> tau_t = 0.1 0.1 0.1 ; time constant, in ps
> ref_t = 323 323 323 ; reference temperature, one for
> each group, in K),
> Is this separate coupling needed at all taking into account that this
> temperature coupling method produces the correct coupling? Is it probably better
> to use a single coupling constant (system) and so avoid problems using this
> artificial correction to deal with the "hot solvent / cold solute" artifact?
Technically the correct way to do it is to use one global thermostat rather than
individual ones, but multiple thermostats are used for the reason described. I
think it is actually more to do with electrostatics approximations than the
thermostat itself (i.e. plain cutoffs leading to poor energy conservation and
thus heating of the solvent, which diffuses rapidly) than anything else, so
using PME is more robust. Someone please correct me if I'm remembering wrong.
I don't recall having seen a test of an inhomogeneous system with a single
thermostat, so multiple thermostats remain common practice. There are numerous,
extensive discussions in the list archive about these topics so I would
encourage you to search around a bit.
> Could somebody kindly tell me how large could the coupling constant, tau_t, be?
> Is it OK to switch, e.g., from 0.1 to 0.3 ps after T equilibration is reached,
> i.e., during the production phase?
This issue is discussed in the reference for the V-rescale thermostat (Bussi et al).
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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