TMD

From: David Wright (david_william_wright_at_yahoo.co.uk)
Date: Thu Jun 21 2007 - 06:03:07 CDT

I've been trying to tun a TMD simulation but I'm getting the following error:

ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: TMDLastStep
ERROR: TMDFirstStep
ERROR: TMDFinalRMSD
ERROR: TMDOutputFreq
ERROR: TMDk
ERROR: TMDFile
ERROR: TMD

I'm probably missing something obvious but can anyone let me know what I'm doing wrong, the conf file I'm using is:

structure ../common/ubq.psf
coordinates ../common/ubq_ww_eq.pdb
outputName ubq_ww_targ

# Continuing a job from the restart
 files
if {1} {
set inputname ubq_ww_pcv
binCoordinates $inputname.restart.coor
binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this!
extendedSystem $inputname.xsc
}

#############################################################
## SIMULATION PARAMETERS ##
#############################################################

# Input
paraTypeCharmm on
parameters ../common/par_all27_prot_lipid.inp

wrapWater
 on
wrapAll on

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5

# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10

#
 Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens

restartfreq 500 ;# 500steps = every 1ps
dcdfreq 500
xstFreq 500
outputEnergies 100
outputPressure 100

#############################################################
## EXTRA
 PARAMETERS ##
#############################################################

# Put here any custom parameters that are specific to
# this job (e.g., SMD, TclForces, etc...)

TMD on
TMDFile ubq_targ.pdb
TMDk 7
TMDOutputFreq 10
TMDFinalRMSD 0
TMDFirstStep 20000
TMDLastStep 40000

#############################################################
## EXECUTION
 SCRIPT ##
#############################################################

run 20000

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