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Sample configuration files

This section contains some simple example NAMD configuration files to serve as templates.

This file shows a simple configuration file for alanin. It performs basic dynamics with no output files or special features.

# protocol params
numsteps        1000

# initial config
coordinates     alanin.pdb
temperature     300K
seed            12345

# output params
outputname      /tmp/alanin
binaryoutput    no

# integrator params
timestep        1.0

# force field params
structure       alanin.psf
parameters      alanin.params
exclude         scaled1-4
1-4scaling      1.0
switching       on
switchdist      8.0
cutoff          12.0
pairlistdist    13.5
stepspercycle   20

This file is again for alanin, but shows a slightly more complicated configuration. The system is periodic, a coordinate trajectory file and a set of restart files are produced.

# protocol params
numsteps        1000

# initial config
coordinates     alanin.pdb
temperature     300K
seed            12345

# periodic cell
cellBasisVector1   33.0 0 0
cellBasisVector2   0 32.0 0
cellBasisVector3   0 0 32.5

# output params
outputname      /tmp/alanin
binaryoutput    no
DCDfreq         10
restartfreq     100

# integrator params
timestep        1.0

# force field params
structure       alanin.psf
parameters      alanin.params
exclude         scaled1-4
1-4scaling      1.0
switching       on
switchdist      8.0
cutoff          12.0
pairlistdist    13.5
stepspercycle   20

This file shows another simple configuration file for alanin, but this time with full electrostatics using PME and multiple timestepping.

# protocol params
numsteps        1000

# initial config
coordinates     alanin.pdb
temperature     300K
seed            12345

# periodic cell
cellBasisVector1   33.0 0 0
cellBasisVector2   0 32.0 0
cellBasisVector3   0 0 32.5

# output params
outputname      /tmp/alanin
binaryoutput    no
DCDfreq         10
restartfreq     100

# integrator params
timestep        1.0
fullElectFrequency  4

# force field params
structure       alanin.psf
parameters      alanin.params
exclude         scaled1-4
1-4scaling      1.0
switching       on
switchdist      8.0
cutoff          12.0
pairlistdist    13.5
stepspercycle   20

# full electrostatics
PME             on
PMEGridSizeX    32
PMEGridSizeY    32
PMEGridSizeZ    32

This file demonstrates the analysis of a DCD trajectory file using NAMD. The file pair.pdb contains the definition of pair interaction groups; NAMD will compute the interaction energy and force between these groups for each frame in the DCD file. It is assumed that coordinate frames were written every 1000 timesteps. See Sec. 15.1 for more about pair interaction calculations.

# initial config
coordinates     alanin.pdb
temperature     0

# output params
outputname      /tmp/alanin-analyze
binaryoutput    no

# integrator params
timestep        1.0

# force field params
structure       alanin.psf
parameters      alanin.params
exclude         scaled1-4
1-4scaling      1.0
switching       on
switchdist      8.0
cutoff          12.0
pairlistdist    13.5
stepspercycle   20
 
# Atoms in group 1 have a 1 in the B column; group 2 has a 2.
pairInteraction		on
pairInteractionFile	pair.pdb
pairInteractionCol	B
pairInteractionGroup1	1
pairInteractionGroup2	2

# First frame saved was frame 1000.
set ts 1000

coorfile open dcd /tmp/alanin.dcd

# Read all frames until nonzero is returned.
while { ![coorfile read] } {
  # Set firstTimestep so our energy output has the correct TS.
  firstTimestep $ts
  # Compute energies and forces, but don't try to move the atoms.
  run 0
  incr ts 1000
}
coorfile close


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