[gmx-users] simulated annealing mdp
ramadavidgroup at gmail.com
Tue Jun 12 15:09:24 CEST 2012
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
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
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..
With Best Wishes,
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