From: Felipe Merino (felipe.merino_at_mpi-dortmund.mpg.de)
Date: Tue Jul 21 2015 - 03:28:40 CDT
Hey,
You should really read the error. You have a typo, outputTiminig instead
of outputTiming.
Felipe
On 21/07/15 09:54, Urszula Uciechowska wrote:
> 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 (Ã
)
> cutoff 12; # only calc short range interactions inside this (Ã
)
> pairlistdist 10; # every stepPerCycle, each atom updates its list
> # of atoms it may be interacting with during
> # the following cycle, using this distance (Ã
)
>
> ## 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
>
>
>
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
-- Felipe Merino Max Planck Institute for Molecular Physiology Department of Structural Biochemistry Otto-Hahn-Str. 11 44227 Dortmund Phone: +49 231 133 2306
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:59 CST