Metadynamics simulation

From: Azadeh Alavi (azade.alavi_at_gmail.com)
Date: Tue Jan 03 2017 - 09:00:43 CST

Dear NAMD users,

I am going to perform Metadynamics simulations for ion transport through a
protein. I am using NAMD2.11. I have copied the input file below.
First, I was wondering if a timestep of 2 fs is OK to run this simulation
and whether the parameters below are reasonable.
Secondly, when I run this simulation, the output file of HillsTrajectory is
empty which is weird.

Thanks a lot for your help.
Azadeh

colvar {
   name Translocation
   lowerBoundary -4.0
   lowerWallConstant 100.0
   upperBoundary 56.0
   upperWallConstant 100.0
   width 0.4
   outputVelocity on
   outputAppliedForce on

   distanceZ {
      main {
         atomnumbers { 131678 }
      }
      ref {
         atomnumbers { protein alpha carbons..
           }
      }
      axis ( 0.0, 0.0, 1.0 )
   }
}

metadynamics {

   colvars Translocation
   hillWeight 0.01 # Default is 0.01 - higher numbers = faster
   newHillFrequency 100 # Default is 100 - lower numbers = faster
   writeFreeEnergyFile on
   saveFreeEnergyFile on
   keephills on
   writeHillsTrajectory on
}

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