vidhya sankar wrote:
Hai justin,
Sorry for the inconvenient posting
I am going to simultaneously do both Simulated annealing as well as
SMD for a folded Protein to explore the stability of proteins at
different mutations because my protein contain more than one chain i
am going to pull as well as do SA Is it possible in gromacs ?
Possible, yes. Useful, not likely. You don't know how the system is going to
respond to either an increase in temperature or the applied force, so mixing the
two is just asking for the simulation to blow up. I also wonder what use the
data would be, even if the simulation runs to completion. To what do you
attribute the effects you see - the high temperature, the applied force, or some
fortuitous combination of annealing rate and pull rate and/or force constant
that give you some interesting result?
I would say forget about SMD and perhaps simply look at thermostability.
There's lots of literature on high-temperature MD and it may be useful for
telling you something about how stable your protein is. Otherwise, search the
literature for other methods, because what you've defined now sounds like a
total crapshoot as to whether or not it will even work.
-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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