NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system

From: Seke Keretsu (
Date: Mon Nov 16 2020 - 01:55:06 CST

Dear Expert,

I am performing a conventional MD simulation of a GPCR-ligand system
consisting approximately 77000 atoms. The 1 ns test run took about 2 days
to complete on a 36 cpu machine (Centos7, intex xeon gold).

I am not sure if this rate is expected.

I wonder if using the parameters/configuration generated from charmm-gui is
slowing my production run. Could someone give an insight into this.
Is there a way to speed up the simulation ?

The system consisted of POPC, solvent and protein-ligand complex totalling
to about 77000 atoms.

The input config file is given below:

structure step5_charmm2namd.psf
coordinates step5_charmm2namd.pdb

set temp 303.15;
outputName step7_production; # base name for output from this
                                            # NAMD writes two files at the
end, final coord and vel
                                            # in the format of
first-dyn.coor and first-dyn.vel

set inputname step6.6_equilibration;
binCoordinates $inputname.coor; # coordinates from last run
binVelocities $inputname.vel; # velocities from last run
extendedSystem $inputname.xsc; # cell dimensions from last run

restartfreq 5000; # 5000 steps = every 10ps
dcdfreq 50000;
dcdUnitCell yes; # the file will contain unit
cell info in the style of
                                            # charmm dcd files. if yes, the
dcd files will contain
                                            # unit cell information in the
style of charmm DCD files.
xstFreq 5000; # XSTFreq: control how often
the extended systen configuration
                                            # will be appended to the XST
outputEnergies 5000; # 5000 steps = every 10ps
                                            # The number of timesteps
between each energy output of NAMD
outputTiming 5000; # The number of timesteps
between each timing output shows
                                            # time per step and time to

# Force-Field Parameters
paraTypeCharmm on; # We're using charmm type
parameter file(s)
                                            # multiple definitions may be
used but only one file per definition
parameters toppar/par_all36m_prot.prm
parameters toppar/par_all36_na.prm
parameters toppar/par_all36_carb.prm
parameters toppar/par_all36_lipid.prm
parameters toppar/par_all36_cgenff.prm
parameters toppar/par_interface.prm
parameters toppar/toppar_all36_nano_lig.str
parameters toppar/toppar_all36_nanolig_patch.str
parameters toppar/toppar_all36_synthetic_polymer.str
parameters toppar/toppar_all36_synthetic_polymer_patch.str
parameters toppar/toppar_all36_polymer_solvent.str
parameters toppar/toppar_water_ions.str
parameters toppar/toppar_dum_noble_gases.str
parameters toppar/toppar_ions_won.str
parameters toppar/toppar_all36_prot_arg0.str
parameters toppar/toppar_all36_prot_c36m_d_aminoacids.str
parameters toppar/toppar_all36_prot_fluoro_alkanes.str
parameters toppar/toppar_all36_prot_heme.str
parameters toppar/toppar_all36_prot_na_combined.str
parameters toppar/toppar_all36_prot_retinol.str
parameters toppar/toppar_all36_prot_modify_res.str
parameters toppar/toppar_all36_na_nad_ppi.str
parameters toppar/toppar_all36_na_rna_modified.str
parameters toppar/toppar_all36_lipid_archaeal.str
parameters toppar/toppar_all36_lipid_bacterial.str
parameters toppar/toppar_all36_lipid_cardiolipin.str
parameters toppar/toppar_all36_lipid_cholesterol.str
parameters toppar/toppar_all36_lipid_dag.str
parameters toppar/toppar_all36_lipid_inositol.str
parameters toppar/toppar_all36_lipid_lps.str
parameters toppar/toppar_all36_lipid_miscellaneous.str
parameters toppar/toppar_all36_lipid_model.str
parameters toppar/toppar_all36_lipid_prot.str
parameters toppar/toppar_all36_lipid_sphingo.str
parameters toppar/toppar_all36_lipid_yeast.str
parameters toppar/toppar_all36_lipid_hmmm.str
parameters toppar/toppar_all36_lipid_detergent.str
parameters toppar/toppar_all36_lipid_ether.str
parameters toppar/toppar_all36_carb_glycolipid.str
parameters toppar/toppar_all36_carb_glycopeptide.str
parameters toppar/toppar_all36_carb_imlab.str
parameters toppar/toppar_all36_label_spin.str
parameters toppar/toppar_all36_label_fluorophore.str
parameters ../unk/unk.prm # Custom topology and parameter
files for UNK
source step5_charmm2namd.str

# These are specified by CHARMM
exclude scaled1-4 # non-bonded exclusion policy
to use "none,1-2,1-3,1-4,or scaled1-4"
                                            # 1-2: all atoms pairs that are
bonded are going to be ignored
                                            # 1-3: 3 consecutively bonded
are excluded
                                            # scaled1-4: include all the
1-3, and modified 1-4 interactions
                                            # electrostatic scaled by
1-4scaling factor 1.0
                                            # vdW special 1-4 parameters in
charmm parameter file.
1-4scaling 1.0
switching on
vdwForceSwitching yes; # New option for force-based
switching of vdW
                                            # if both switching and
vdwForceSwitching are on CHARMM force
                                            # switching is used for vdW

# You have some freedom choosing the cutoff
cutoff 12.0; # may use smaller, maybe 10.,
with PME
switchdist 10.0; # cutoff - 2.
                                            # switchdist - where you start
to switch
                                            # cutoff - where you stop
accounting for nonbond interactions.
                                            # correspondence in charmm:
                                            # (cutnb,ctofnb,ctonnb =
pairlistdist 16.0; # stores the all the pairs with
in the distance it should be larger
                                            # than cutoff( + 2.)
stepspercycle 20; # 20 redo pairlists every ten
pairlistsPerCycle 2; # 2 is the default
                                            # cycle represents the number
of steps between atom reassignments
                                            # this means every 20/2=10
steps the pairlist will be updated

# Integrator Parameters
timestep 2.0; # fs/step
rigidBonds all; # Bound constraint all bonds
involving H are fixed in length
nonbondedFreq 1; # nonbonded forces every step
fullElectFrequency 1; # PME every step

wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
if { $boxtype == "hexa" } {
wrapNearest on; # use for non-rectangular cells
(wrap to the nearest image)
} else {
wrapNearest off; # use for non-rectangular cells
(wrap to the nearest image)

# PME (for full-system periodic electrostatics)
PME yes;
PMEInterpOrder 6; # interpolation order (spline
order 6 in charmm)
PMEGridSpacing 1.0; # maximum PME grid space / used
to calculate grid size

# Constant Pressure Control (variable volume)
useGroupPressure yes; # use a hydrogen-group based
pseudo-molecular viral to calcualte pressure and
                                            # has less fluctuation, is
needed for rigid bonds (rigidBonds/SHAKE)
useFlexibleCell yes; # yes for anisotropic system
like membrane
useConstantRatio yes; # keeps the ratio of the unit
cell in the x-y plane constant A=B

langevinPiston on; # Nose-Hoover Langevin piston
pressure control
langevinPistonTarget 1.01325; # target pressure in bar 1atm =
langevinPistonPeriod 50.0; # oscillation period in fs.
correspond to pgamma T=50fs=0.05ps
                                            # f=1/T=20.0(pgamma)
langevinPistonDecay 25.0; # oscillation decay time.
smaller value correspons to larger random
                                            # forces and increased coupling
to the Langevin temp bath.
                                            # Equall or smaller than piston
langevinPistonTemp $temp; # coupled to heat bath

# Constant Temperature Control
langevin on; # langevin dynamics
langevinDamping 1.0; # damping coefficient of 1/ps
(keep low)
langevinTemp $temp; # random noise at this level
langevinHydrogen off; # don't couple bath to hydrogens
# run
numsteps 500000; # 1ns run stops when this step
is reached
run 500000; # 1ns

Thank you.

seke keretsu

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