Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 1

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Apr 11 2016 - 10:02:45 CDT

Most of the NAMD configuration options specify the physical description of
your system, and should not change if you add metadynamics or other
external forces.

Giacomo

On Sat, Apr 9, 2016 at 1:03 PM, Sourav Ray <souravray90_at_gmail.com> wrote:

> I am planning to run a metadynamics simulation for 200 ns with 0.5 fs time
> step (is it ok or shall I increase the time step?) 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 NAMD conf file I have written.
>
>
> ###################################################
> # EQUILIBRATION
> ###################################################
>
>
> # INPUT
>
> parameters martini (all necessary ones)
> paraTypeCharmm on
>
> structure solvate.psf
> coordinates equil.coor
> velocities equil.vel
>
> #bincoordinates mm.coor
> #binvelocities mm.vel
> #extendedsystem equil.xsc
>
> temperature 310.0
>
>
> # Force-Field Parameters
>
> exclude 1-2
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> martiniSwitching on
> PME off
> switchdist 9.0
> pairlistdist 14.0
> dielectric 15.0
> nonbondedFreq 1
> stepspercycle 10
>
>
> # CELL
>
> cellbasisvector1 90 0 0
> cellbasisvector2 0 90 0
> cellbasisvector3 0 0 90
> cellOrigin 45.000 45.000 45.000
>
> wrapAll off
>
>
> # COM
>
> commotion no
> zeroMomentum yes
>
>
> # CONSTANT-T
>
> langevin on
> langevinTemp 300.0
> langevinDamping 1.0
> rescaleTemp 300.0
> rescaleFreq 500
>
>
> # OUTPUT
>
> outputname mlt_meta
> restartname mlt_meta
>
> outputenergies 100000
> outputtiming 100000
> outputpressure 100000
> restartfreq 100000
> XSTFreq 100000
> dcdFreq 100000
>
>
> # METADYNAMICS SECTION
>
> colvars on
> colvarsConfig gyration_rmsd.in
>
>
> # MD SETUP
>
> timestep 0.5
> numSteps 400000000
>
> Thanks and regards
> Sourav
>

-- 
Giacomo Fiorin
Assistant Professor of Research
Institute for Computational Molecular Science (ICMS)
College of Science and Technology, Temple University
1925 North 12th Street (035-07), Room 704D
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Phone: +1-215-204-4213
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Personal: http://giacomofiorin.github.io/
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*"As computer programmers we have a responsibility to make sure that we run
the computers instead of the computers running us."*  - Steve Oualline

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