From: Mauricio Carrillo Tripp (trippm_at_wabash.edu)
Date: Mon Jun 07 2004 - 11:46:18 CDT
Hi all,
I'm trying to run a simulation calculating a pressure profile.
I followed the manual's directions and it doesn't seem to be working.
When a try to run I get the message:
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.
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Charmrun> All clients connected.
Charmrun> IP tables sent.
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.5 for Linux-i686-TCP
Info:
Info: Running on 16 processors.
Info: 1476 kB of memory in use.
Measuring processor speeds... Done.
Info: Configuration file is config_restart.namd
TCL: Suspending until startup complete.
Warning: The following variables were set in the
Warning: configuation file but were not needed
Warning: pressureprofilenonbonded
Warning: pressureprofileslabs
Warning: pressureprofilefreq
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: pressureProfileOn
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
Stack Traceback:
[0] _ZN9NamdState14configListInitEP10ConfigList+0x294 [0x81fb274]
[1] _ZN9ScriptTcl9initcheckEv+0x59 [0x822afa1]
[2] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x1e [0x8228ff6]
[3] TclInvokeStringCommand+0x6d [0x82c27b5]
[4] /usr/local/NAMD_2.5_Linux-i686-TCP/namd2 [0x82f6ada]
[5] Tcl_EvalEx+0x1cc [0x82f71ec]
[6] Tcl_EvalFile+0x157 [0x82ef353]
[7] _ZN9ScriptTcl3runEPc+0x1a [0x8228976]
[8] main+0x1d2 [0x80ece52]
[9] __libc_start_main+0xe4 [0x42015574]
[10] sinh+0x69 [0x80eacd1]
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If I don't use the "pressureProfile" options everything runs fine. My
config file is
as follows:
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structure dppc.psf
coordinates dppc.pdb
set temperature 323 ;# target temperature used several times below
# continuing a run
set inputname test03.restart ;# only need to edit this in one place!
outputName test04 ;# base name for output from this run
binCoordinates $inputname.coor ;# coordinates from last run (binary)
binVelocities $inputname.vel ;# velocities from last run (binary)
extendedSystem $inputname.xsc ;# cell dimensions from last run
firsttimestep 6000 ;# last step of previous run
numsteps 506000 ;# run stops when this step is reached
restartfreq 500 ;# 500 steps = every 1ps
dcdfreq 500
dcdUnitCell yes ;# the file will contain unit cell info in the
style of charmm dcd files
xstFreq 500
outputEnergies 100 ;# 100 steps = every 0.2 ps
outputTiming 100 ;# shows time per step and time to completion
outputPressure 100 ;#
# Force-Field Parameters
paraTypeCharmm on
parameters param.inp
# These are specified by CHARMM
exclude scaled1-4
1-4scaling 1.0
switching on
# You have some freedom choosing the cutoff
cutoff 10. ;# may use smaller, maybe 10., with PME
switchdist 9. ;# cutoff - 2.
# Promise that atom won't move more than 2A in a cycle
pairlistdist 15. ;# cutoff + 2.
stepspercycle 20 ;# redo pairlists every ten steps
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1 ;# nonbonded forces every step
fullElectFrequency 2 ;# PME only every other step
# Constant Temperature Control
langevin on ;# langevin dynamics
langevinDamping 5. ;# damping coefficient of 5/ps
langevinTemp $temperature ;# random noise at this level
langevinHydrogen no ;# don't couple bath to hydrogens
# Periodic Boundary conditions. Used only when first starting, not on a
restart
#cellBasisVector1 44.60686 0. 0. ;# vector to the next image
#cellBasisVector2 0. 58.96183 0.
#cellBasisVector3 0. 0 65.01609
cellOrigin 0. 0. 0. ;# the *center* of the cell
wrapWater on ;# wrap water to central cell
wrapAll on ;# wrap other molecules too
wrapNearest off ;# use for non-rectangular cells
#PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 45 ;# 3^2 * 5, close to 44.6
PMEGridSizeY 64 ;# 2^6 , close to 58.9
PMEGridSizeZ 81 ;# 3^4 , close to 65.01
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigid bonds
useFlexibleCell yes ;# no for water box, yes for membrane
useConstantArea yes ;# no for water box, maybe for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# pressure in bar -> 1 atm
langevinPistonPeriod 100. ;# oscillation period around 100 fs
langevinPistonDecay 50. ;# oscillation decay time of 50 fs
langevinPistonTemp $temperature ;# coupled to heat bath
# Pressure Profile Calculation
pressureProfileOn on
pressureProfileSlabs 80
pressureProfileFreq 100
pressureProfileNonbonded off
run 500000
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Any help would be appreciated.
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Mauricio Carrillo Tripp
Chemistry Department
Wabash College
http://chem.acad.wabash.edu/~trippm
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