[gmx-users] simulated annealing mdp

[rama david]

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..


With Best Wishes,
Rama David.
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