Dear Anju,
You can do simulated annealing using weight restraints to control the value
of temp0. E.g.
/
&wt type='TEMP0', istep1=0,istep2=100000,
value1=0.0, value2=150.0, /
&wt type='END' /
For a tutorial on simulating DNA see:
http://amber.scripps.edu/tutorials/basic/tutorial1/index.htm
Beyond that for protocols regarding simulated annealing I suggest you
consult the literature.
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Anju Sharma
Sent: Tuesday, April 03, 2007 05:27
To: amber.scripps.edu
Subject: AMBER: Regarding Simulated Annealing
Hello frnds,
I want to carry out simulated annealing of my DNA sequence. Can any one
suggest me how to do dis. Is dere any help or tutorial available online
regarding dis.
Waiting for response
--
Anju Sharma
Project Fellow,
NIT, Hamirpur (H.P.)
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Received on Wed Apr 04 2007 - 06:07:46 PDT
