nvt run error

From: Urszula Uciechowska (urszula.uciechowska_at_biotech.ug.edu.pl)
Date: Tue Jul 21 2015 - 02:54:10 CDT

hi,

I am getting an error when I try to run nvt simulations which is:

Info: NAMD 2.9 for Linux-x86_64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60400 for net-linux-x86_64-gcc
Info: Built Thu Feb 13 13:19:02 CET 2014 by soft on n1017-amd.zeus
Info: 1 NAMD 2.9 Linux-x86_64 1 zeus.cyfronet.pl cg2uciec
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00501204 s
Info: 1.49986 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is nvt.namd
Info: Working in the current directory
/mnt/lustre/scratch2/people/cg2uciec/NAMD-DNA/model-4
TCL: Suspending until startup complete.
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: outputTiminig
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE

My input file:
## USER VARIABLES
set outPrefix output/model4-nvt
set inPrefix output/model4-npt.restart
set temperature 300

##Output
outputName nvt; # this tells namd where to write output files

##Number of steps between output writes
dcdfreq 1000; # simulation trajectory
restartfreq 500; # 500 steps = every 1ps
xstFreq 500; # XSTFreq: control how often the extended
system configuration will be appended to the XST file
outputEnergies 125; # 125 steps = every 0.25ps
outputPressure 125; # info about the pressure (printed in log file)
outputTiminig 500; # the number of timsteps between each
timinig output shows the time per step and time to completion

##Input
structure ssb.psf; # initial structure file
coordinates ssb.pdb; # initial coordinate file

cellBasisVector1 86.313 0 0
cellBasisVector2 0 88.430 0
cellBasisVector3 0 0 83.732

firstTimeStep 0; # only affects dynamics for SMD simulations

##Restart files
binCoordinates min.coor
binVelocities min.vel

COMmotion yes; # always (default is no and removes the
center
                                # of mass velocity whenever you restart a
simulation

#Constant pressure simulation
langevinPiston on; # turn this off for constant volume sim
langevinPistonTarget 1.01325; # in bar -> 1 atm
langevinPistonPeriod 50
langevinPistonDecay 25
langevinPistonTemp $temperature

#Constant Temperature Control
langevin on; # langevin dynamics
langevinDamping 3.0; # dumping coefficient
langevinTemp $temperature
langevinHydrogen no; # do not couple the bath to hydrogens

## additional
useGroupPressure yes; # yes = don't
                              # needed for rigidBonds (see rigidBonds below)
useFlexibleCell no; # allow x,y,z dimensions to fluctuate
independently?
# useConstantArea no; # if so, fix area of xy-plane?
# useConstantRatio no; # OR if so, fix aspect ratio of xy-plane?

## affects output coordinates only, not dynamics
# wrapAll on; # since we use periodic boundary conditions
we keep everything in one unit cell
wrapWater on

##FORCES##

## multiple timestepping: calculate some forces less frequently
timestep 2; # use 2fs timestep (for bonded interactions)
                         # all the other "frequencies" (really periods)
                         # are in terms of this

nonBondedFreq 1; # vdW and short range electrostatics every 2fs
fullElectFrequency 1; # long range electrostatics every 6fs
stepsPerCycle 20; # re-evaluate parilistdist after this many steps
pairlistsPerCycle 2; # default value

## bonded interactions
rigidBonds all; # freezes bond length between hydrogen and other
atoms
                          # which is the fastest vibrational mode in an MD
sim

exclude scaled1-4; # scale vdW interaction for bonded
atoms
1-4scaling 1.0; # use 0.833333333 for Amber parameters

## short-range interactions
switching on; # smoothly turn off vdW interactions at cutoff
vdwForceSwitching yes; # new option for force-based switching of vdw
switchDist 10; # start turning vdW interaction off (Å)
cutoff 12; # only calc short range interactions inside this (Å)
pairlistdist 10; # every stepPerCycle, each atom updates its list
                         # of atoms it may be interacting with during
                         # the following cycle, using this distance (Å)

## long-range interactions (particle-mesh ewald for long-range
electrostatics)
PmeGridSpacing 2.0; # this is larger than the usual number
PME yes
PMEGridSizeX 120
PMEGridSizeY 120
PMEGridSizeZ 120

## Force-Field Parameters
paraTypeCharmm on; # we always use CHARMM
formatted parameters (even when using Amber)
parameters par_all36_na.prm; # parameter file specifies
how atoms should interact
parameters par_all36_prot.prm; # parameter file specifies
how atoms should interact
parameters par_water_ions_na.prm; # parameter file specifies
how atoms should interact

###Run
minimize 2500
run 25000

What is wrong in the input file.

best regards
Urszula

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