From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue May 10 2016 - 15:25:18 CDT
Hello Sourav the two boundaries define the grid but you want to activate
the optional wallconstant keywords to make the boundaries repulsive.
Your changes in hill height and frequency are simply adding more energy to
the system and accelerating the sampling further.
Giacomo
On May 5, 2016 6:34 AM, "Sourav Ray" <souravray90_at_gmail.com> wrote:
> 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
>
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