Issue regarding to the speed of QM/MM

From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Mon Sep 07 2020 - 03:40:03 CDT

Dear all,
I am running a enzyme complex (298 amino acid and 1 ligand and 90 thousand water molecules ) molecular dynamic simulation by QM/MM using NAMD, but it is very slowly with which only 25 steps being done every day (24 hours) in a

minimization simulation (minimize 100, run 2000), I wonder if there are some isses regarding to the parameters of config file, any suggestion to improve the speed for running QM/MM will be much appreciated.

The hardware for my computer (8173M workstation) is fine with 384GB memory and two physical memory (28 core per CPU, and 112 threads) , the command is as follows:

charmrun ++local +p20 +isomalloc_sync namd2 YZZ-config.ORCA-1.namd | tee YZZ-config.ORCA-1.namd.log

Thank you in advance.

Zhihong Xin,

The config file is as follows:
## Single QM region with MM water box
structure ionized.psf
coordinates ionized.pdb
#Continuing a job from the restart files
if {1} {
set inputname YZZ_equil_MM
binCoordinates $inputname.coor
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 2.0
# 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
# Number of simultaneous QM simulations per node
QMSimsPerNode 20
QMElecEmbed on
QMSwitching on
QMSwitchingType shift
QMPointChargeScheme none
QMBondScheme "cs"
#qmBaseDir "/dev/shm/YZZ-NAMD_MIN"
# Directory where QM calculations will be ran.
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"
#qmConfigLine "%%pal nprocs 10 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



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