From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Tue Sep 01 2020 - 21:10:17 CDT
Deal Namd,
I came across a issue when I run a QM/MM simulation，
TCL: Minimizing for 100 steps
Info: List of ranks running QM simulations: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9.
[file orca_tools/Tool-GTO-Bases/basissets.cpp, line 706]: Wrong number of basis-sets stored!
FATAL ERROR: Error reading QM forces file.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error reading QM forces file.
I do not find the solution in the mailing list and ask for help, any suggestion will be much appreciate.
My Namd config file as follows:
# This is a namd configuration file
## Single QM region with MM water box
structure ./ionized.psf
coordinates ./YZZ-namd-equil-last-1.pdb
# Continuing a job from the restart files
if {1} {
set inputname ../YZZ_equil_MM
binCoordinates $inputname.coor
#binVelocities $inputname.vel ;# remove the "temperature" entry if you use this!
extendedSystem $inputname.xsc
}
cellBasisVector1 64.945 0 0
cellBasisVector2 0 65.353 0
cellBasisVector3 0 0 67.919
cellOrigin 55.318 57.874 55.561
seed 7910881
# Output Parameters
binaryoutput no
outputname ./YZZ-QM-min-out
outputenergies 1
outputtiming 1
outputpressure 1
binaryrestart yes
dcdfile ./YZZ-QM-min-out.dcd
dcdfreq 1
XSTFreq 1
restartfreq 100
restartname ./YZZ-QM-min-out.restart
# mobile atom selection:
constraints on
consexp 2
consref ./YZZ-restraint.pdb
conskfile ./YZZ-restraint.pdb
conskcol B
constraintScaling 5.0
# PME Parameters
PME on
PMEGridspacing 1
set temperature 300
temperature $temperature
# Thermostat Parameters
langevin on
langevintemp $temperature
langevinHydrogen on
langevindamping 50
# Barostat Parameters
usegrouppressure yes
useflexiblecell no
useConstantArea no
langevinpiston on
langevinpistontarget 1.01325
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp $temperature
surfacetensiontarget 0.0
strainrate 0. 0. 0.
wrapAll on
wrapWater on
# Integrator Parameters
timestep 0.5
firstTimestep 0
fullElectFrequency 1
nonbondedfreq 1
# Force Field Parameters
paratypecharmm on
parameters ../CHARMpars/toppar_all36_carb_glycopeptide.str
parameters ../CHARMpars/toppar_water_ions_namd.str
parameters ../CHARMpars/toppar_all36_na_nad_ppi_gdp_gtp.str
parameters ../CHARMpars/par_all36_carb.prm
parameters ../CHARMpars/par_all36_cgenff.prm
parameters ../CHARMpars/par_all36_lipid.prm
parameters ../CHARMpars/par_all36_na.prm
parameters ../CHARMpars/par_all36_prot.prm
parameters ../common/DMP_ABD769.prm
#printExclusions on
exclude scaled1-4
1-4scaling 1.0
rigidbonds none
cutoff 12.0
pairlistdist 14.0
switching on
switchdist 10.0
stepspercycle 1
# Truns ON or OFF the QM calculations
qmForces on
qmParamPDB "./YZZ-namd-QM-0.pdb"
qmColumn "beta"
qmBondColumn "occ"
#Link Atoms
#qmBondDist on
#qmLinkElement
# Number of simultaneous QM simulations per node
QMSimsPerNode 10
QMElecEmbed on
QMSwitching on
QMSwitchingType shift
QMPointChargeScheme none
QMBondScheme "cs"
qmBaseDir "/dev/shm/NAMD_Example1"
## ORCA
qmConfigLine "! B3LYP 6-31G Grid4 PAL4 EnGrad TightSCF"
qmConfigLine "%%output PrintLevel Mini Print\[ P_Mulliken \] 1 Print\[P_AtCharges_M\] 1 end"
# construction of ORCA's input file.
qmMult "1 2"
qmCharge "1 -1"
qmSoftware "orca"
qmExecPath "/home/xzhfood/software/orca_4_1_2_linux_x86-64_openmpi313/orca"
QMOutStride 1
QMPositionOutStride 1
# Number of steps in the QM/MM simulation.
minimize 100
run 2000
Zhihong Xin
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