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