NAMD Wiki: TestPage5

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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.