Differences between ABF and metadynamics

From: Alex (alniagap_at_gmail.com)
Date: Tue Sep 13 2011 - 05:13:34 CDT

Hi,
I have got different free energy surfaces obtained by using adaptive
biasing force method and metadyanmics calculations for the same
molecule (paracetamol) in vacuum. Could you explain to me why? The
duration of the simulated trajectory was 25 ns after equilibration.
Difference between configurations of calculations only in colvars
configurations.

ABF colvars config contains lines like these:
##################################################
colvarsTrajFrequency 500
colvarsRestartFrequency 500
colvar {
  name phi
  width 5.0
  lowerboundary -180
  upperboundary 180
  dihedral {
    oneSiteSystemForce
    group1 {
      atomnumbers 6
    }
    group2 {
      atomnumbers 5
    }
    group3 {
      atomnumbers 7
    }
    group4 {
      atomnumbers 9
    }
  }
}
colvar {
  name psi
  width 5.0
  lowerboundary -180
  upperboundary 180
  dihedral {
    oneSiteSystemForce
    group1 {
      atomnumbers 5
    }
    group2 {
      atomnumbers 7
    }
    group3 {
      atomnumbers 9
    }
    group4 {
      atomnumbers 10
    }
  }
}
abf {
  colvars phi psi
  fullSamples 200
}
##################################################

Metadynamics colvars config contains lines like these:
##################################################
colvarsTrajFrequency 500
colvarsRestartFrequency 500
colvar {
  name phi
  width 5.0
  lowerboundary -180
  upperboundary 180
  dihedral {
    oneSiteSystemForce
    group1 {
      atomnumbers 6
    }
    group2 {
      atomnumbers 5
    }
    group3 {
      atomnumbers 7
    }
    group4 {
      atomnumbers 9
    }
  }
}
colvar {
  name psi
  width 5.0
  lowerboundary -180
  upperboundary 180
  dihedral {
    oneSiteSystemForce
    group1 {
      atomnumbers 5
    }
    group2 {
      atomnumbers 7
    }
    group3 {
      atomnumbers 9
    }
    group4 {
      atomnumbers 10
    }
  }
}
metadynamics {
  colvars phi psi
  hillWidth 2
}
##################################################

Where phi and psi is the dihedral angles.

Simulations config contains lines like these:
##################################################
numSteps 50000000
structure system.psf
coordinates system.pdb
set temperature 313
set outputname out_system_1
set inputname out_system
binCoordinates $inputname.coor
binVelocities $inputname.vel
firsttimestep 0
paraTypeCharmm on
parameters par_all36_cgenff.prm
exclude scaled1-4
1-4scaling 1.0
cutoff 14.0
switching on
switchdist 10.0
pairlistdist 18.5
timestep 0.5
rigidBonds none
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
langevin on
langevinDamping 5
langevinTemp $temperature
langevinHydrogen on
wrapAll on
outputName $outputname
restartfreq 500
dcdfreq 500
xstFreq 500
outputEnergies 500
outputPressure 500
colvars on
colvarsConfig colvars.in
##################################################

Equilibrations config contains lines like these:
##################################################
structure system.psf
coordinates system.pdb
set temperature 313
set outputname out_system
firsttimestep 0
paraTypeCharmm on
parameters par_all36_cgenff.prm
temperature $temperature
exclude scaled1-4
1-4scaling 1.0
cutoff 14.0
switching on
switchdist 10.0
pairlistdist 18.5
timestep 0.5
rigidBonds none
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
langevin on
langevinDamping 5
langevinTemp $temperature
langevinHydrogen on
wrapAll on
outputName $outputname
restartfreq 500
dcdfreq 500
xstFreq 500
outputEnergies 500
outputPressure 500
minimize 500
reinitvels $temperature
run 10000000
##################################################

PDB file of the molecule:
###############################################################################
ATOM 1 C14 PACP 1 16.078 10.242 15.441 1.00 0.00 PACP C
ATOM 2 H141 PACP 1 16.509 10.274 14.677 1.00 0.00 PACP H
ATOM 3 H142 PACP 1 16.407 10.180 16.325 1.00 0.00 PACP H
ATOM 4 H143 PACP 1 15.840 11.289 15.469 1.00 0.00 PACP H
ATOM 5 C15 PACP 1 14.790 9.463 15.330 1.00 0.00 PACP C
ATOM 6 O29 PACP 1 13.986 9.378 16.260 1.00 0.00 PACP O
ATOM 7 N21 PACP 1 14.595 8.870 14.144 1.00 0.00 PACP N
ATOM 8 H211 PACP 1 15.297 8.939 13.578 1.00 0.00 PACP H
ATOM 9 C22 PACP 1 13.511 8.034 13.744 1.00 0.00 PACP C
ATOM 10 C23 PACP 1 12.251 8.048 14.333 1.00 0.00 PACP C
ATOM 11 H231 PACP 1 12.091 8.657 15.016 1.00 0.00 PACP H
ATOM 12 C24 PACP 1 11.251 7.197 13.873 1.00 0.00 PACP C
ATOM 13 H241 PACP 1 10.346 7.257 14.243 1.00 0.00 PACP H
ATOM 14 C26 PACP 1 12.755 6.339 12.207 1.00 0.00 PACP C
ATOM 15 H261 PACP 1 12.920 5.762 11.471 1.00 0.00 PACP H
ATOM 16 C27 PACP 1 13.742 7.183 12.672 1.00 0.00 PACP C
ATOM 17 H271 PACP 1 14.614 7.182 12.269 1.00 0.00 PACP H
ATOM 18 C25 PACP 1 11.503 6.336 12.818 1.00 0.00 PACP C
ATOM 19 O28 PACP 1 10.485 5.500 12.416 1.00 0.00 PACP O
ATOM 20 H281 PACP 1 10.673 5.217 11.599 1.00 0.00 PACP H
END
###############################################################################

-- 
with best regards,
Alex

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