From: Prince, Chandler (david.prince_at_wustl.edu)
Date: Mon Dec 14 2020 - 11:24:57 CST
I hit reply instead of reply all. It's NAMD 2.13
I've experimented with changing wrapAll to off, but I get the same results. I appreciate your help.
# NAMD i/o file
set sys clc_test
set i 1
set j [expr $i - 1]
set charmmdir charmm-ff-master/
set nsteps 500
# --- integration ---
numsteps $nsteps
timestep 2.0
firsttimestep 0
# --- input files ---
paraTypeCharmm on
parameters $charmmdir/par_all36m_prot.prm
parameters $charmmdir/par_all36_lipid.prm
parameters $charmmdir/par_all36_na.prm
parameters $charmmdir/par_all36_carb.prm
parameters $charmmdir/par_all36_cgenff.prm
parameters $charmmdir/par_water_ions.prm
structure w.all.psf
if { $i == 1 } {
coordinates w.all.pdb
temperature 310.00
} else {
coordinates $sys.equil.$j.coor
bincoordinates $sys.equil.$j.rst.coor
binvelocities $sys.equil.$j.rst.vel
}
# --- output files ---
binaryoutput no
outputname $sys.equil.$i
restartname $sys.equil.$i.rst
restartfreq 500
restartsave no
binaryrestart yes
DCDfile $sys.equil.$i.dcd
DCDfreq 100
DCDUnitCell yes
# --- stdout options ---
outputEnergies 500
mergeCrossterms no
outputMomenta 0
outputPressure 0
outputTiming 500
# --- langevin options ---
langevin on
langevinTemp 310.00
langevinDamping 1
langevinHydrogen off
# --- pressure ---
useGroupPressure yes
useFlexibleCell yes
useConstantArea no
useConstantRatio yes
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 50
LangevinPistonTemp 310.00
# --- constraints ---
rigidBonds all
rigidTolerance 0.00000001
rigidIterations 100
useSettle on
# -- non-bonded interactions ---
exclude scaled1-4
1-4scaling 1.0
switching on
vdwForceSwitching on
switchdist 10
cutoff 12
dielectric 1.0
PME yes
PMETolerance 0.000001
PMEInterpOrder 6
PMEGridSizeX 170
PMEGridSizeY 170
PMEGridSizeZ 70
# -- MTS --
nonbondedFreq 1
fullElectFrequency 1
# --- non-bonded list ---
stepspercycle 10
pairlistdist 14
pairlistsPerCycle 2
pairlistShrink 0.01
pairlistGrow 0.01
pairlistTrigger 0.30
# --- boundary options ---
if { $i == 1 } {
extendedSystem prev.xsc
} else {
extendedSystem $sys.equil.$j.rst.xsc
}
XSTfile $sys.equil.$i.xst
XSTfreq 500
wrapWater on
wrapAll on
wrapNearest on
# --- constraints ---
constraints off
# -- patch control ---
twoAwayX no
twoAwayY no
twoAwayZ no
# --- collective variables ---
colvars on
colvarsConfig RMSD.each.CA.colvar
# --- center-of-mass, distance restraints ---
tclForces on
tclForcesScript tcl_all.inp
________________________________
From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
Sent: Monday, December 14, 2020 8:35 AM
To: NAMD list <namd-l_at_ks.uiuc.edu>; Prince, Chandler <david.prince_at_wustl.edu>
Subject: Re: namd-l: I frequently get FATAL ERROR: Unable to open text file clc_test.equil.1.colvars.state: File exists when running across multiple nodes
Hi Chandler, this could be a bug solved in NAMD 2.13 and later. Which version of NAMD are you using, and what are your output frequencies for both NAMD and Colvars?
On Mon, Dec 14, 2020 at 9:23 AM Prince, Chandler <david.prince_at_wustl.edu<mailto:david.prince_at_wustl.edu>> wrote:
Reason: FATAL ERROR: Unable to open text file clc_test.equil.1.colvars.state: File exists
In this case I'm using LSF, 16 CPUs across two hosts with a GPU on each host. I get this error or one like it every time I attempt to run.
Does anyone have suggestions on what the causes could be?
-Chandler
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