[gmx-users] Coulomb and Lennnard-Jones parameters
Justin Lemkul
jalemkul at vt.edu
Thu Mar 27 13:34:44 CET 2014
On 3/27/14, 6:24 AM, Maria Astón Serrano wrote:
> 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.
Why?
> 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?
>
The W3-W3 identifier indicates a lot of time was spent computing the nonbonded
interactions between water molecules. Looks like you have lots of water and
that's where mdrun spent most of its time.
The input settings (especially rlist, rcoulomb, and rvdw) are a function of the
force field, not your desires for performance. Making changes can lead to
artifacts. Performance increases as a function of decreasing cutoffs, but at
the great cost of large errors.
-Justin
>
> 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
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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