NAMD Wiki: TestPage5
Some placeholder text for this test page 5 (five). Testing...
Some NAMD config lines without heredoc delimiters:
coordinates alanin.pdb temperature 0
outputname /tmp/alanin-analyze binaryoutput no
timestep 1.0
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
pairInteraction on pairInteractionFile pair.pdb pairInteractionCol B pairInteractionGroup1 1 pairInteractionGroup2 2
set ts 1000
coorfile open dcd /tmp/alanin.dcd
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
And now with heredoc style delimiters.
# 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
An edit after the above table of NAMD config file.