collective variable calculation from dcd file

From: Giovanni Bellesia (
Date: Wed Dec 21 2011 - 14:44:47 CST

Hi all,

I'm wondering if it's possible to calculate a collective variable (i.e., a
dihedral calculated over 4 groups of atoms)
from a dcd trajectory file.
I am pasting the configuration file I am trying to use.
What it does is ... it computes the state of the variable at the first step
and then it stops with error message "Segmentation default"




structure ./structure.psf
coordinates ./coords.pdb

set temperature 310
set outputname out1

firsttimestep 0

# Input
paraTypeCharmm on
vdwGeometricSigma yes
parameters ./opls.prm
temperature $temperature

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0

# Constant Temperature Control
langevin on
langevinDamping 1.0
langevinTemp $temperature
langevinHydrogen no

# GBIS parameters
ionConcentration 0.3
alphaCutoff 12

# Nonbonded parameters
switching on
switchdist 12
cutoff 13
pairlistdist 14.5

# Multistep parameters
timestep 2.0
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

colvars on

outputName $outputname
binaryOutput no

set ts 1

coorfile open dcd test1.dcd

# Read all frames until nonzero is returned.
while { ![coorfile read] } {.
  firstTimestep $ts
  run 0
  incr ts 1
coorfile close

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:05 CST