Restarting the NAMD Simulation?

Hi! When you prepare input files (.namd extension), you can set the appropriate restart information.

Important things to set are:

- restart options (restartfreq - parameter that specifies how frequently the program writes restart files during the simulation; dcdfreq and xstfreq that do the same action, but on different output files)

- binaryrestart (binary format file that contains the complete state of a simulation at a specific point in time)

- outputname (name you want for your files)

Basically you have a input.namd like this (it's an example):

----------------------

# NAMD input file

# Structure and parameter files

structure protein.psf

coordinates protein.pdb

parameters par_all36m_prot.prm

# Output

restartfreq 1000

dcdfreq 1000

xstfreq 1000

outputEnergies 1000

binaryoutput yes

binaryrestart yes

outputname simulation

dcdfile simulation.dcd

xstfile simulation.xst

# Force field and integrator

timestep 2.0

exclude scaled1-4

1-4scaling 1.0

switching on

switchdist 10.0

cutoff 12.0

# Temperature and pressure control

temperature 300

langevin on

langevinDamping 5.0

langevinTemp 300

# Run parameters

numsteps 10000

rigidBonds all

rigidTolerance 0.00001

nonbondedFreq 1

# Periodic boundary conditions

cellBasisVector1 80.0 0.0 0.0

cellBasisVector2 0.0 80.0 0.0

cellBasisVector3 0.0 0.0 80.0

cellOrigin 0.0 0.0 0.0

wrapAll on

# PME (Particle Mesh Ewald) for long-range electrostatics

PME on

PMEGridSpacing 1

----------------------

Of course you have to modify this file according to your molecule and to your purposes. Hope this helps!

Dinesh Kumar J

Kumar Pratyush as Davide Pietrafesa mentioned, assume that your first input file, file1.namd contains the above parameters. After the successful completion of the file1.namd or from wherever you want to continue the simulation in the new file, file2.namd add the below parameters

set inputname simulation #outputname given in file1.namd

binCoordinates $inputname.restart.coor

binVelocities $inputname.restart.vel # remove the "temperature"

extendedSystem $inputname.xsc

firsttimestep 4000000 #Mention the timestep from where you want to continue the simulation.

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