pair interaction calculations

From: Xin Chen (
Date: Thu Jul 29 2004 - 17:18:36 CDT

Dear NAMD users,

I try to use the configuration file for pair interaction at:

But got a error message like this:

Info: Configuration file is pairs.namd
Warning: Couldn't parse line 60 in configuration file pairs.namd. The line
was: }
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: incr
ERROR: run
ERROR: while
ERROR: coorfile
ERROR: set

It seems that the NAMD can not recognize the command like "run", "set" in
the configuration file. It even cannot recognize "}". How we can make it
recognize them?

The configuration file is as follows:

# 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

Sincerely yours,

Xin Chen

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