[gmx-users] reg SA cum SMD

[Justin A. Lemkul]

vidhya sankar wrote:
> Dear justin., Thank you tfor your reply
>                       Can i combine Simulated annealing protocol with 
> SMD . if possible what Time factor should i  consider to avoid Clashes 
> in Md simulation i am asking whether any relation between time of 
> pulling and time of annealing should i have awareness ?  when seeinf 
> input files

You haven't provided nearly enough information to get a useful reply.  What do 
you mean "combine?"  Are you running SA before, during, or after SMD?  What are 
your objectives?  What is in your system?  Without knowledge of all of these 
things, no one can suggest anything about time.  Evolution of dynamics for 
separating two ions in water will be considerably faster (orders of magnitude, 
in fact) than pulling a ligand through a heteromultimeric protein complex 
embedded in a multicomponent lipid membrane.

Without knowing far more about what you're doing, I'm not going to speculate.

-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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