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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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