From: Urszula Uciechowska (urszula.uciechowska_at_biotech.ug.edu.pl)
Date: Fri Jul 24 2015 - 03:27:31 CDT
Dear all,
I got an error message while running nvt:
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Infiniband support is active.
Namd ibverbs will be loaded by 'apps/namd/2.9'.
'compilers/gcc/4.8.0' load complete.
'tools/openmpi/1.6.5-gnu-4.8.0-ib' load complete.
'apps/namd/2.9' load complete.
'tools/scratch/1.0' load complete.
Charmrun> started all node programs in 1.054 seconds.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Incorrect atom count in binary file min.coor
Fatal error on PE 0> FATAL ERROR: Incorrect atom count in binary file
min.coor
mpiexec: killing job...
I checked the number of atoms and is the same. What did go wrong?
My input file for nvt run was:
## 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)
outputTiming 500; # the number of timsteps between each
timinig output shows the time per step and time to completion
##Input
structure model4_wbI.psf; # initial structure file
coordinates model4_wbI.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 5.0; # 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 (<C3><85>)
cutoff 12; # only calc short range interactions inside this
(<C3><85>)
pairlistdist 16; # every stepPerCycle, each atom updates its list
# of atoms it may be interacting with during
# the following cycle, using this distance
(<C3><85>)
# Harmonic constraints
constraints on;
consexp 2;
conskcol B;
conskfile restrained.pdb;
consref model4_wbI.pdb;
constraintScaling 10; #scale values in "0-columns by a factor 10
## 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
Thank you for any suggestions.
best regards
Urszula
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland
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