protein folding by simulated anneling

From: Puspita Halder (
Date: Mon May 28 2012 - 01:11:53 CDT

Hi all,

I have posted an e-mail in the namd mailing list regarding protein folding
study using simulated annealing technique few days back. But I am yet to
get any reply from anyone of you. I am writing it once again.

I have been working on protein folding problem for the last few months. I
have some high temperature (400K, 500K) euilibrated trajectories of my
protein with which I would like to adopt the simulated annealing run. Is
this doable beacause in most of the cases I saw that this technique employs
the heating as well as the cooling phase. Can I skip the heating phase if I
start directly from the high temerature structures ? Another thing is what
should be the ideal step size for temperature decrease and the number of
iterations for each step in the loop by using this method?

If you have answers for my queries then please respond.



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