James Starlight wrote:
Justin,
Could you tell me for what purposes the definition of the several ref_t
values could be usefull? Does this just for measurements of the
temperature during simulation for each group separately or is there
something else?
Each ref_t value is the target temperature for however many groups you have
assigned to separate thermostats.
By the way as I've found in literature another important question about
such simulation in high temperature conditions is the selection of the
integrator algorithm wich also could enhanse sampling under this
conditions. E.g I've found that the BD integrator could be more usefull
than leap-frog MD. What timestep and other importnat options defined in
mdp should be tken into account within simulation with BD ? I've never
perform simulations with this integrator and could not realise how it
could enhanse simulation rate in comparison to the MD and what artifacts
should expect from that :)
I have never used the bd integrator so I cannot offer any help here. I don't
see any magical reason why you should expect it to enhance sampling though.
-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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