Troubles with Free Energy of Conformation Change

From: Masya Mix (masya.mix_at_gmail.com)
Date: Thu Apr 26 2007 - 14:23:13 CDT

Hello,

I want to calculate the free energy of conformation change of torsion angle
in DNA but I've confronted by difficulties with getting the value of free
energy.
Where can I find this value to be written? What way is being used for the
calculating of this free energy?

P.S. Below my script:

freeEnergy on

freeEnergyConfig {

urestraint {

    dihe (DNAA, 414, O5') (DNAA, 414, C5') (DNAA, 414, C4') (DNAA,414, C3')
barr=20 ref=60
    }

    pmf {
       task = grow
       time = 300 ps
       print = 1 ps
    }
    pmf {
       task = stop
       time = 300 ps
    }
    pmf {
       task = fade
       time = 300 ps
   }
}

Maria
Graduat student
Kharkov National Univesity
Department of Biological and Medical physics
Email: *masya.mix_at_gmail.com*

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