Metadynamics simulation with Radius of Gyration and RMSD variation - 1

From: Sourav Ray (souravray90_at_gmail.com)
Date: Sat Apr 09 2016 - 12:03:36 CDT

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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

• Next message: Sourav Ray: "Metadynamics simulation with Radius of Gyration and RMSD variation - 2"
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• Next in thread: Giacomo Fiorin: "Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 1"
• Reply: Giacomo Fiorin: "Re: Metadynamics simulation with Radius of Gyration and RMSD variation - 1"
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