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.