From: Sourav Ray (souravray90_at_gmail.com)
Date: Sat Apr 09 2016 - 14:53:15 CDT
Also, is it appropriate to consider the backbone or certain central atoms
for radius of gyration variation or shall we consider all the atoms on the
peptide chain?
On Sat, Apr 9, 2016 at 10:41 PM, Sourav Ray <souravray90_at_gmail.com> wrote:
> 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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