From: matziast_at_med.uth.gr
Date: Fri Oct 15 2010 - 06:35:37 CDT
Hi,
I need again your help, I want to run TMD with the following script:
#############################################################
## JOB DESCRIPTION ##
#############################################################
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure initial.psf
coordinates initial.pdb
bincoordinates eq_x.coor
binvelocities eq_x.vel
set outputname TMD_nomin
firsttimestep 0
numsteps 100000
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_x.inp
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 8.
pairlistdist 13.5
margin 0
# Integrator Parameters
timestep 1.0 ;# 1fs/step
rigidBonds all ;# needed for 1fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
# Output
outputName $outputname
dcdfreq 1000
outputEnergies 10
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Boundary conditions
#wrapWater on
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 300
langevinHydrogen off ;# don't couple langevin bath to hydrogens
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Targeted
TMD on
TMDk 200
TMDFirstStep 0
TMDLastStep 100000
TMDfile target.pdb
TMDFinalRMSD 0
and I received the following log file:
Charm++: standalone mode (not using charmrun)
Info: NAMD 2.5 for Win32-i686
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 050612 for net-win32-smp
Info: Running on 2 processors.
Info: 0 kB of memory in use.
Measuring processor speeds... Done.
Info: Configuration file is tmd_script_2.txt
TCL: Suspending until startup complete.
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: TMDFinalRMSD
ERROR: TMDfile
ERROR: TMDLastStep
ERROR: TMDFirstStep
ERROR: TMDk
ERROR: TMD
Please I need your help, any comment is acceptable.
Thank you.
Maria
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