[gmx-users] simulated annealing mdp

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 12 15:14:04 CEST 2012

On 6/12/12 9:09 AM, rama david wrote:
> Hello Justin and Ravi,
> Lets explain me Why I  did simulated anealing?? ..
> I synthesise peptide and I have experimental data for its self assembly,
> I just want to reproduced these data.
> I arranged the 32 protein in axis to petide fibre, in antiparrallel Beta sheet
> structure.
> I dont have crystal structure ,
> Thats why I did SA in the hope that after these the side chain may be get
> properly oriented with respect to each other.That will give me good structure
> for production run.
>   I also run system withought SA , but I get good result by following SA  protocol.
> In posrestrain only backbone is restrained and the sidechain is free to move, So I
> think it may be help to achieve my goal.
> After these I also plan  to use SA as production run, then compare the result
> with previous protocols.
> Please give valuable suggestion to improve my study protocol..

Seems reasonable.  Stating this up front in the original message would have 
saved some time.  Otherwise, we make assumptions ;)



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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