Re: pmf

From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Tue Jan 11 2005 - 19:24:04 CST

Hi Swarna,
   Their is relatively good documentation and discussions on this. Here is
the portion I add to my namd configuration file, it holds the two methane
centers (carbon) at a fixed distance using harmonic restraints. I then use
the WHAM equations to combine the results to get the free energy curve.

# restraints to hold methanes apart
freeEnergy on
freeEnergyConfig {
     urestraint {
dist pmf (CH4,821,C)(CH4,822,C) kf=25, low=8.5, hi=3.2
  }

   mcti
     {
     task = stepup
     equiltime = 60000 fs
     accumtime = 100000 fs
     numsteps = 27
     print = 1000 fs
     }
   mcti
     {
     task = stepdown
     }
   }

Ed

On Wed, 12 Jan 2005, Swarna Patra wrote:

> hi
> can anyone help me in pmf calculation...I am not able to set the
> configuration file correctly..please give me a sample configurationfile if
> anyone has.
> thanks
> swarna
>
>

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