Hyunjin Kim wrote:
Hi,
Gromacs manual says that when "SD" used
as a thermostat, an appropriate value for "tau_t" is 2 ps, since this
results in a friction that is lower than the internal friction of water,
while it is high enough to remove excess heat (unless cut-off or
reaction-field electrostatics is used). However, the free energy tutorial
uses the smaller "tau_t" value, so I wonder whether I have to use 2 ps.
Some reference discussions:
http://lists.gromacs.org/pipermail/gmx-users/2009-February/039508.html
http://lists.gromacs.org/pipermail/gmx-users/2008-February/032341.html
http://lists.gromacs.org/pipermail/gmx-users/2008-October/037339.html
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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