pmf command

From: Pedro Swagger (pedrito.swagger_at_gmail.com)
Date: Wed Jul 24 2013 - 15:30:40 CDT

Hello Experts,

Could anyone explain the following command? or Point out in which part of
the manual they are explain? .

I tried to search for them on the namd website but I did not find anything?
I dont understand inside the loop pmf {} and what are they are they 3 pmf
serial.

thanks

#############################################################
## EXTRA PARAMETERS ##
#############################################################

# conformational free energies
### 10 ps growing time as per NAMD user guide example
### use pulling speed of 0.1 A/ps as per NAMD tutorial, p. 68
freeEnergy on
freeEnergyConfig {
   urestraint {
      dist pmf (BH, 1, N) (BH, 10, NT) kf=7.2 low=13 hi=33
   }
   pmf {
   task = grow
   time = 10 ps
   }
   pmf {
   task = up
   time = 200 ps
   print = 1 ps
   }
   pmf {
   task = stop
   time = 10 ps
   }
   pmf {
   task = down
   time = 200 ps
   print = 1 ps
   }
} 

-- 
Pedro
Saludos
Departamento de Física,
Facultad de Ciencias,
Universidad de Chile
Las Palmeras 3425, Ñuñoa, Santiago, Chile

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