gradual increase in the temperature after minimization

From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Wed Dec 09 2009 - 12:21:34 CST

Dear all,
I know that this question has been posted earlier , since it was not clear
to me, i am posting the doubt .

1. The config file is similar to the one from the NAMD tutorial and i have
modified it slightly to increase the temperature gradually by including the
temperature reassignmnent parameters like this :
reassignTemp 25
reassignIncr 5
reassignHold 310
reassignFreq 1000

I have attached the complete file as protein.conf.
>From the earlier posts, they have mentioned as to comment out the langevin
dynamics temperature control parameters. Since I want to keep the
temperature constant during the simulation. does the ReassignHold parameter
serves the purpose of Constant temperature control parameter?

2 .and also i have tried one more strategy to increase the temperature by
including the following terms after minimization step :
minimize 5000
for {set i 0} {$i <= $temperature} {incr i 10} {
langevinTemp $i
langevinPistonTemp $i
run 500
}

I have attached the complete config file as attachment.(protein1.conf)
But this seems to work properly, as the avg temperature is near to 310
immediately after minimization.

Kindly look into it and provide any corrections or suggestions in the
config file so that it serves the purpose.

Thank you,
Gurunath

-- 
Gurunath M Katagi
Graduate Research Student
Bio molecular computation Laboratory
Supercomputer Education & Research Center
Indian Institute Of Science, Bangalore- 560012
Karnataka State, India
Phone:080-22932737-319,080-22933061
email: gurunath_at_rishi.serc.iisc.ernet.in


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