[gmx-users] Coulomb and Lennnard-Jones parameters
Maria Astón Serrano
m.aston.serrano at gmail.com
Thu Mar 27 11:25:21 CET 2014
Dear Gromacs users
I would like to ask for your advice concerning to the input parameters for
a simulation. I am simulating a protein (1L2Y,
http://www.rcsb.org/pdb/explore/explore.do?structureId=1L2Y). I obtain the
timing results below.
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-Cycles Seconds %
-----------------------------------------------------------------------
Comm. coord. 8 100001 198.994 58.7 1.0
Neighbor search 8 20001 1402.166 413.3 7.3
Force 8 100001 10529.644 3103.9 54.6
Wait + Comm. F 8 100001 331.925 97.8 1.7
PME mesh 8 100001 6183.435 1822.8 32.0
Write traj. 8 101 3.434 1.0
0.0
Update 8 100001 148.251 43.7 0.8
Constraints 8 100001 304.236 89.7 1.6
Comm. energies 8 20002 36.774 10.8 0.2
Rest 8 162.448 47.9
0.8
-----------------------------------------------------------------------
Total 8 19301.307 5689.7
100.0
-----------------------------------------------------------------------
-----------------------------------------------------------------------
PME redist. X/F 8 200002 3957.969 1166.7 20.5
PME spread/gather 8 200002 1502.640 443.0 7.8
PME 3D-FFT 8 200002 477.460 140.7 2.5
PME solve 8 100001 242.220 71.4 1.3
-----------------------------------------------------------------------
Parallel run - timing based on wallclock.
I was expecting the constraint time to take above 15% of the total time.
However, I find just 1.6%. I suspect that perhaps the parameters for the
Coulomb and Lennnard-Jones calculation may be improved: In the md.log file,
I find:
Computing: M-Number M-Flops
% Flops
------------------------------------------------------------
---------------------------------
Coul(T) + LJ [W3-W3] 18217.759964 6959184.306 76.8
Is this wise? May you give me a hint on how to tune the parameters?
These are my input parameters:
integrator = md
nsteps = 100000
init_step = 0
ns_type = Grid
nstlist = 5
ndelta = 2
nstcomm = 10
comm_mode = Linear
nstlog = 1000
nstxout = 1000
nstvout = 1000
nstfout = 0
nstcalcenergy = 5
nstenergy = 1000
nstxtcout = 1000
init_t = 0
delta_t = 0.002
xtcprec = 1000
nkx = 28
nky = 28
nkz = 28
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = xyz
bPeriodicMols = FALSE
bContinuation = TRUE
bShakeSOR = FALSE
etc = V-rescale
nsttcouple = 5
epc = Parrinello-Rahman
epctype = Isotropic
nstpcouple = 5
tau_p = 2
ref_p (3x3):
ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}
compress (3x3):
compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}
refcoord_scaling = No
posres_com (3):
posres_com[0]= 0.00000e+00
posres_com[1]= 0.00000e+00
posres_com[2]= 0.00000e+00
posres_comB (3):
posres_comB[0]= 0.00000e+00
posres_comB[1]= 0.00000e+00
posres_comB[2]= 0.00000e+00
andersen_seed = 815131
rlist = 1
rlistlong = 1
rtpi = 0.05
coulombtype = PME
rcoulomb_switch = 0
rcoulomb = 1
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 1
epsilon_r = 1
epsilon_rf = 1
tabext = 1
implicit_solvent = No
gb_algorithm = Still
gb_epsilon_solvent = 80
nstgbradii = 1
rgbradii = 1
gb_saltconc = 0
gb_obc_alpha = 1
gb_obc_beta = 0.8
gb_obc_gamma = 4.85
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension = 2.05016
DispCorr = EnerPres
free_energy = no
init_lambda = 0
delta_lambda = 0
n_foreign_lambda = 0
sc_alpha = 0
sc_power = 0
sc_sigma = 0.3
sc_sigma_min = 0.3
nstdhdl = 10
separate_dhdl_file = yes
dhdl_derivatives = yes
dh_hist_size = 0
dh_hist_spacing = 0.1
nwall = 0
wall_type = 9-3
wall_atomtype[0] = -1
wall_atomtype[1] = -1
wall_density[0] = 0
wall_density[1] = 0
wall_ewald_zfac = 3
pull = no
disre = No
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Shake
shake_tol = 0.0001
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 601.892 16092.1
ref_t: 300 300
tau_t: 0.1 0.1
anneal: No No
ann_npoints: 0 0
acc: 0 0 0
nfreeze: N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
Table routines are used for coulomb: TRUE
Table routines are used for vdw: FALSE
Will do PME sum in reciprocal space.
Thank you very much.
Maria
More information about the gromacs.org_gmx-users
mailing list