[gmx-users] SA and smd

[Justin A. Lemkul]

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

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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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