From: Sourav Ray (souravray90_at_gmail.com)
Date: Thu May 05 2016 - 05:33:26 CDT
Hello
I have used the colvar module below to perform my Metadynamics run. In
spite of setting an "upperboundary", the rmsd and gyration values are
crossing the same and are somehow in sync with each other w.r.t. their
values vs time. I have kept both "wrapall" on and off conditions, but it
was same for both the cases.
*Note: *I have changed "hillWeight" from 0.01 to 0.1 and
"newHillFrequency" from 1000 to 100. Is any or both of these modifications
causing this? Before making these changes, I didn't observe this situation.
colvarsTrajFrequency 10000
colvarsRestartFrequency 10000
colvar {
name RMSD
width 0.5
lowerboundary 0.0
upperboundary 50.0
expandBoundaries off
outputAppliedForce on
rmsd {
atoms {
atomsfile rmsd_backbone.pdb
atomsCol B
atomsColValue 10.00
}
refPositionsFile rmsd_backbone.pdb
refPositionsCol B
refPositionsColValue 10.00
}
}
colvar {
name GYRA
width 0.5
lowerboundary 10.0
upperboundary 50.0
expandBoundaries off
outputAppliedForce on
gyration {
atoms {
atomsfile gyration_backbone.pdb
atomsCol B
atomsColValue 10.00
}
}
}
metadynamics {
colvars RMSD GYRA
hillWeight 0.1
newHillFrequency 100
writeHillsTrajectory on
hillWidth 2
}
Thanks and regards
Sourav
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:06 CST