Re:Re: Issue regarding to the speed of QM/MM

From: 辛志宏 (
Date: Tue Sep 08 2020 - 07:20:57 CDT

Many thanks Marcelo,Alexander and axel for your suggestion and explanation.

1. My workstation just for molecule dynamic calculation and no other task for use.

2. There are 135 QM atoms in the present simulation,

Info: Number of QM atoms (excluding Dummy atoms): 135
Info: We found 9 QM-MM bonds.
Info: Applying user defined multiplicity 2 to QM group ID 1
Info: 1) Group ID: 1 ; Group size: 135 atoms ; Total PSF charge: -1
Info: Found user defined charge -1 for QM group ID 1. Will ignore PSF charge.
Info: MM-QM pair: 2163:2165 -> Value (distance or ratio): 1 (QM Group 0 ID 1)
Info: MM-QM pair: 2176:2174 -> Value (distance or ratio): 1 (QM Group 0 ID 1)
Info: MM-QM pair: 2854:2856 -> Value (distance or ratio): 1 (QM Group 0 ID 1)
Info: MM-QM pair: 2875:2873 -> Value (distance or ratio): 1 (QM Group 0 ID 1)
Info: MM-QM pair: 3558:3556 -> Value (distance or ratio): 1 (QM Group 0 ID 1)
Info: MM-QM pair: 3572:3574 -> Value (distance or ratio): 1 (QM Group 0 ID 1)
Info: MM-QM pair: 3593:3591 -> Value (distance or ratio): 1 (QM Group 0 ID 1)
Info: MM-QM pair: 4002:4004 -> Value (distance or ratio): 1 (QM Group 0 ID 1)
Info: MM-QM pair: 4021:4019 -> Value (distance or ratio): 1 (QM Group 0 ID 1)
Info: ****************************
Info: 29430 ATOMS
Info: 21182 BONDS
Info: 16615 ANGLES
Info: 12135 DIHEDRALS
Info: TOTAL MASS = 181629 amu
Info: TOTAL CHARGE = 1 e
Info: MASS DENSITY = 1.04522 g/cm^3
Info: ATOM DENSITY = 0.10199 atoms/A^3
Info: *****************************

3. I re-setup the QM parameters as follows:

QMSimsPerNode 40
qmConfigLine "! B3LYP 6-31G Grid4 PAL16 EnGrad TightSCF"

The performance is improved 4 times (25 steps/6hours) than the original one (25 steps/24hours),

but when I setup the QM parmeters as "PAL20" or higher than 20, an fetal error for QM force calculation occured,I don't know why the error occur,because there are the total 56 cores.

Are there any other method to further improve the performance by adjust config parameters?

The command is "charmrun ++local +p40 +isomalloc_sync namd2 YZZ-config.ORCA-1.namd | tee YZZ-config.ORCA-1.namd.log"

Thanks in advance.

Zhihong Xin

发件人:"Marcelo C. R. Melo" <>
发送日期:2020-09-08 02:11:07
收件人:NAMD <>,"辛志宏" <>
主题:Re: namd-l: Issue regarding to the speed of QM/MM
Hi Zhihong,

The performance of a QM/MM simulation will (almost always) be determined by the performance of the QM calculation itself. In this case, you are using ORCA to run DFT using 4 CPU cores (by asking for "PAL4").

In QM calculations, it is important to know what is the size of the QM region, that is, how many atoms are in the QM region? 10 atoms, 100 atoms? This will make a gigantic difference in performance.

The best bet for you is to balance the number of cores dedicated to NAMD with the number of cores dedicated to ORCA, and absolutely never overlap the CPU cores for both.
Something else that has been discussed in this list extensively is the use of hiperthreading. In your example, since you have two 28-core CPUs, you should only allocate a total of 56 processes between NAMD and ORCA, no more than that. Using all the 112 threads will probably lead to terrible performance.

I would suggest starting with 10 cores for NAMD and 46 for ORCA. (I am assuming based on your performance that you have many atoms in your QM region, which will benefit from more CPU cores).
You will need to use ORCA's long format for parallelism instead of using "PAL4", and I see you already have a line like that in your NAMD config file asking for 10 cores.
Try benchmarking the ratio of NAMD/ORCA CPU cores, and do not exceed 56 (or maybe 54, to leave a couple of cores for the OS, since you are running in a workstation).


On Mon, 7 Sep 2020 at 04:42, 辛志宏 <> wrote:

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"
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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