Metadynamics simulation with Radius of Gyration and RMSD variation - 2

From: Sourav Ray (souravray90_at_gmail.com)
Date: Sat Apr 09 2016 - 12:11:53 CDT

I am planning to run a metadynamics simulation to test the stability of a
coarse-grained peptide/protein quartet. It would be really helpful if
someone can give me a feedback regarding the COLVARS file I have written.

I actually don't understand the correlation between colvarsTrajFrequency
and colvarsRestartFrequency with the simulation run time (as in how these
relate with the chosen simulation time step). Also, can anyone suggest
typical upper and lower wallconstants to be used for gyration and rmsd
calculations?

colvarsTrajFrequency 500
colvarsRestartFrequency 500

colvar {
  name RMSD
  width 0.1 #Check again
  lowerboundary 0.0
  upperboundary 50.0
  lowerwallconstant 100.0
  upperwallconstant 100.0
  outputAppliedForce on

  rmsd {
    atoms {
      atomsfile rmsd_pos.pdb
      atomsCol B
      atomsColValue 100.00
    }
    refPositionsFile rmsd_ref.pdb
    refPositionsCol B
    refPositionsColValue 100.00
  }

}

colvar {
  name GYRA
  width 0.1 #Check again
  lowerboundary 0.0
  upperboundary 50.0
  lowerwallconstant 100.0
  upperwallconstant 100.0
  outputAppliedForce on

  rmsd {
    atoms {
      atomsfile rgyr_pos.pdb
      atomsCol B
      atomsColValue 100.00
    }
    refPositionsFile rgyr_ref.pdb
    refPositionsCol B
    refPositionsColValue 100.00
  }

}

metadynamics {
  colvars phi psi
  hillWidth 2
}

Thanks and regards
Sourav

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