simulated annealing script

From: Cheri M Turman (
Date: Thu Sep 25 2003 - 13:15:10 CDT

Hi all,
I am having trouble with a simulated annealing protocol. I would like
to heat my system from 300K to 600K in 2ps, hold at 600K for 10ps, and
cool from 600K to 0K in 20ps. The reassigment part of my NAMD script is
as follows:

timestep 2
# protocol
reassignFreq 167
reassignTemp 250
reassignIncr 50
reassignHold 600
minimize 20000
run 6000

reassignFreq 833
reassignTemp 550
reassignIncr -50
reassignHold 0
run 10000

The heating and holding at 600K works but it does not heat gradually
over 2ps, rather it heats to 600K almost immediately (ie 40 steps). The
cooling part does not run at all. The program aborts giving:
FATAL ERROR: Setting parameter reassignFreq from script failed! I may
not be really understanding the parameters reassignFreq, reassingTemp,
etc. I have spent a great deal of time trying to figure these out. Can
anyone give me a pointer?

   Cheri M. Turman
   Graduate Student
   University of Texas-Houston Medical School
    6431 Fannin
    Houston, TX 77030

    Ph.: 713-500-6126
    Fax: 713-500-0652

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