Hello all,
I am doing a production MD run of a protein-ligand complex in explicit
water with GROMACS4.6.5
However, I got different coulomb cutoff values as shown in the output log
files.
1st one:
...................................................................................................................................
NOTE: Turning on dynamic load balancing
step 60: timed with pme grid 112 112 112, coulomb cutoff 1.000: 235.9
M-cycles
step 100: timed with pme grid 100 100 100, coulomb cutoff 1.116: 228.8
M-cycles
step 100: the domain decompostion limits the PME load balancing to a
coulomb cut-off of 1.162
step 140: timed with pme grid 112 112 112, coulomb cutoff 1.000: 223.9
M-cycles
step 180: timed with pme grid 108 108 108, coulomb cutoff 1.033: 219.2
M-cycles
step 220: timed with pme grid 104 104 104, coulomb cutoff 1.073: 210.9
M-cycles
step 260: timed with pme grid 100 100 100, coulomb cutoff 1.116: 229.0
M-cycles
step 300: timed with pme grid 96 96 96, coulomb cutoff 1.162: 267.8
M-cycles
step 340: timed with pme grid 112 112 112, coulomb cutoff 1.000: 241.4
M-cycles
step 380: timed with pme grid 108 108 108, coulomb cutoff 1.033: 424.1
M-cycles
step 420: timed with pme grid 104 104 104, coulomb cutoff 1.073: 215.1
M-cycles
step 460: timed with pme grid 100 100 100, coulomb cutoff 1.116: 226.4
M-cycles
optimal pme grid 104 104 104, coulomb cutoff 1.073
DD step 24999 vol min/aver 0.834 load imb.: force 2.3% pme mesh/force
0.687
...................................................................................................................................
2nd one:
NOTE: Turning on dynamic load balancing
step 60: timed with pme grid 112 112 112, coulomb cutoff 1.000: 187.1
M-cycles
step 100: timed with pme grid 100 100 100, coulomb cutoff 1.116: 218.3
M-cycles
step 140: timed with pme grid 112 112 112, coulomb cutoff 1.000: 172.4
M-cycles
step 180: timed with pme grid 108 108 108, coulomb cutoff 1.033: 188.3
M-cycles
step 220: timed with pme grid 104 104 104, coulomb cutoff 1.073: 203.1
M-cycles
step 260: timed with pme grid 112 112 112, coulomb cutoff 1.000: 174.3
M-cycles
step 300: timed with pme grid 108 108 108, coulomb cutoff 1.033: 184.4
M-cycles
step 340: timed with pme grid 104 104 104, coulomb cutoff 1.073: 205.4
M-cycles
step 380: timed with pme grid 112 112 112, coulomb cutoff 1.000: 172.1
M-cycles
step 420: timed with pme grid 108 108 108, coulomb cutoff 1.033: 188.8
M-cycles
optimal pme grid 112 112 112, coulomb cutoff 1.000
DD step 24999 vol min/aver 0.789 load imb.: force 4.7% pme mesh/force
0.766
...................................................................................................................................
The 2nd MD run turned out to be much faster (5 times), and the reason I
submitted the 2nd is because the 1st was unexpectedly slow.
I made sure the .tpr file and .pbs file (MPI for a cluster, which consists
of Xeon E5649 CPUs) are virtually identical, and here is my .mdp file:
;
title = Production Simulation
cpp = /lib/cpp
; RUN CONTROL PARAMETERS
integrator = md
tinit = 0 ; Starting time
dt = 0.002 ; 2 femtosecond time step for integration
nsteps = 500000000 ; 1000 ns = 0.002ps * 50,000,000
; OUTPUT CONTROL OPTIONS
nstxout = 25000 ; .trr full precision coor every
50ps
nstvout = 0 ; .trr velocities output
nstfout = 0 ; Not writing forces
nstlog = 25000 ; Writing to the log file every 50ps
nstenergy = 25000 ; Writing out energy information
every 50ps
energygrps = dikpgdu Water_and_ions
; NEIGHBORSEARCHING PARAMETERS
cutoff-scheme = Verlet
nstlist = 20
ns-type = Grid
pbc = xyz ; 3-D PBC
rlist = 1.0
; OPTIONS FOR ELECTROSTATICS AND VDW
rcoulomb = 1.0 ; short-range electrostatic cutoff (in
nm)
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; interpolation
fourierspacing = 0.12 ; grid spacing for FFT
vdw-type = Cut-off
rvdw = 1.0 ; short-range van der Waals cutoff (in
nm)
optimize_fft = yes ;
; Temperature coupling
Tcoupl = v-rescale
tc-grps = dikpgdu Water_and_ions
tau_t = 0.1 0.1
ref_t = 298 298
; Pressure coupling
Pcoupl = Berendsen
Pcoupltype = Isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
; OPTIONS FOR BONDS
continuation = yes
constraints = hbonds
constraint-algorithm = Lincs
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
I am surprised that the coulomb cutoffs of 1.073 vs 1.000 could cause
5-fold performance difference, and why would they be different in the first
place if identical input files were used?
I haven't found anything peculiar on the cluster I am using.
Any suggestions for the issue?
Thanks,
Yun
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