[gmx-users] Gromacs version for polarizable model
Justin Lemkul
jalemkul at vt.edu
Wed Jun 22 15:43:11 CEST 2016
On 6/22/16 3:11 AM, Luca Banetta wrote:
> Dear all,
> I am trying to use a polarizable model for acetone molecule. After
> lots of attempts we created a stable model for a single acetone
> molecule in a sea of water running the simulation on one core.
> So then we started new simulations with a certain number of acetone
> molecules and the simulation appeared to run, but unfortunately it
> doesn't write anything in log file, xtc or trr files.
>
The SCF approach to doing polarizable simulations (the only thing supported in
GROMACS until my Drude branch is ready for merge - I'm working out the last bug,
hopefully) is VERY expensive. Simulations can be orders of magnitude slower
than comparable additive systems due to the many additional force calls that are
required to relax the shells. This gets exacerbated in the case of using only
one core.
You can try increasing the simulation output (nstlog, nstxtcout, etc) to confirm
that it's still running or use verbose mode (mdrun -v) to see the progress in
real time.
-Justin
> Is this a problema connected with an old version of the code (4.5.4)
> that I used?
> If yes, which code should I get?
>
> In thw following lines I show:
>
> TOPOLOGY
>
> #include "oplsaaff.itp"
> #include "oplsaa.ff/spc.itp"
> [ moleculetype ]
> ; Name nrexcl
> acetone 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr
> charge mass typeB chargeB massB
> 1 opls_280 1 LIG C 1 -0.47 12.011
> 2 opls_135 1 LIG C 2 -0.18 12.011
> 3 opls_135 1 LIG C 3 -0.18 12.011
> 4 opls_281 1 LIG O 1 0.47
> 15.5994
> 5 opls_282 1 LIG H 2 0.06 1.008
> 6 opls_282 1 LIG H 2 0.06 1.008
> 7 opls_282 1 LIG H 2 0.06 1.008
> 8 opls_282 1 LIG H 3 0.06 1.008
> 9 opls_282 1 LIG H 3 0.06 1.008
> 10 opls_282 1 LIG H 3 0.06 1.008
> 11 SP 1 LIG SP 1 -0.47 0.400
> 12 VS 1 LIG VS 1 0.47 0.000
>
> [ polarization ]
> ; atom shell functiontype alpha nm^3
> 4 11 1 0.001
>
> [ bonds ]
> ; ai aj funct c0 c1 c2 c3
> 1 2 1
> 1 3 1
> 1 4 1
> 1 12 6
> 2 5 1
> 2 6 1
> 2 7 1
> 2 12 6
> 3 8 1
> 3 9 1
> 3 10 1
> 3 12 6
> 4 11 1
>
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
> 2 8 1
> 2 9 1
> 2 10 1
> 3 5 1
> 3 6 1
> 3 7 1
> 4 5 1
> 4 6 1
> 4 7 1
> 4 8 1
> 4 9 1
> 4 10 1
>
> [ angles ]
> ; ai aj ak funct c0 c1 c2 c3
> 2 1 3 1
> 2 1 4 1
> 3 1 4 1
> 1 2 5 1
> 1 2 6 1
> 1 2 7 1
> 5 2 6 1
> 5 2 7 1
> 6 2 7 1
> 1 3 8 1
> 1 3 9 1
> 1 3 10 1
> 8 3 9 1
> 8 3 10 1
> 9 3 10 1
>
> [ dihedrals ]
> ; ai aj ak al funct c0 c1
> c2 c3 c4 c5
> 3 1 2 5 3
> 3 1 2 6 3
> 3 1 2 7 3
> 4 1 2 5 3
> 4 1 2 6 3
> 4 1 2 7 3
> 2 1 3 8 3
> 2 1 3 9 3
> 2 1 3 10 3
> 4 1 3 8 3
> 4 1 3 9 3
> 4 1 3 10 3
>
> [ exclusions ]
> ; interazioni di non legame tra il primo atomo e i successivi non sono
> considerate
> 1 2 3 4 5 6 7 8 9 10 11 12
> 2 3 4 5 6 7 8 9 10 11 12
> 3 4 5 6 7 8 9 10 11 12
> 4 5 6 7 8 9 10 11 12
> 5 6 7 8 9 10 11 12
> 6 7 8 9 10 11 12
> 7 8 9 10 11 12
> 8 9 10 11 12
> 9 10 11 12
> 10 11 12
> 11 12
>
> [ virtual_sites2 ]
> ; site ai aj funct a
> 12 1 4 1 -0.30
>
>
> [ system ]
> mixture
>
> [ molecules ]
> acetone 150
> SOL 1359
>
> MDP FILE
>
> ; VARIOUS PREPROCESSING OPTIONS
> title = Yo
> cpp = /usr/bin/cpp
> include =
> define =
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.0001
> nsteps = 1000000
> ; For exact run continuation or redoing part of a run
> init_step = 0
> ; mode for center of mass motion removal
> comm-mode = Linear
> ; number of steps for center of mass motion removal
> nstcomm = 1
> ; group(s) for center of mass motion removal
> comm-grps =
>
> ; LANGEVIN DYNAMICS OPTIONS
> ; Temperature, friction coefficient (amu/ps) and random seed
> ;ref-t = 300
> bd-fric = 0
> ld-seed = 1993
>
> ; ENERGY MINIMIZATION OPTIONS
> ; Force tolerance and initial step-size
> emtol = 100
> emstep = 0.01
> ; Max number of iterations in relax_shells
> niter = 20
> ; Step size (1/ps^2) for minimization of flexible constraints
> fcstep = 0
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep = 1000
> nbfgscorr = 10
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout =
> nstvout =
> nstfout =
> ; Checkpointing helps you continue after crashes
> nstcheckpoint = 1000
> ; Output frequency for energies to log file and energy file
> nstlog = 50
> nstenergy = 50
> ; Output frequency and precision for xtc file
> nstxtcout = 1
> xtc-precision = 1000
> ; This selects the subset of atoms for the xtc file. You can
> ; select multiple groups. By default all atoms will be written.
> xtc-grps =
> ; Selection of energy groups
> energygrps =
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 20
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)
> ; or full (infinite systems only)
> pbc = xyz
> ; nblist cut-off
> rlist = 1.2
> domain-decomposition = no
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = PME
> rcoulomb-switch = 0
> rcoulomb = 1.2
> ; Dielectric constant (DC) for cut-off or DC of reaction field
> epsilon-r = 1
> ; Method for doing Van der Waals
> vdw-type = Cut-off
> ; cut-off lengths
> rvdw-switch = 0
> rvdw = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension = 1
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.16
> ; FFT grid size, when a value is 0 fourierspacing will be used
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
>
> ; GENERALIZED BORN ELECTROSTATICS
> ; Algorithm for calculating Born radii
> gb_algorithm = Still
> ; Frequency of calculating the Born radii inside rlist
> nstgbradii = 1
> ; Cutoff for Born radii calculation; the contribution from atoms
> ; between rlist and rgbradii is updated every nstlist steps
> rgbradii = 2
> ; Salt concentration in M for Generalized Born models
> gb_saltconc = 0
>
> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> implicit_solvent = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> Tcoupl = v-rescale
> ; Groups to couple separately
> tc-grps = System
> ; Time constant (ps) and reference temperature (K)
> tau_t = 0.1
> ref_t = 300
> ; Pressure coupling
> Pcoupl = berendsen
> Pcoupltype = isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
> ; Random seed for Andersen thermostat
> andersen_seed = 815131
>
> ; SIMULATED ANNEALING
> ; Type of annealing for each temperature group (no/single/periodic)
> annealing = no
> ; Number of time points to use for specifying annealing in each group
> annealing_npoints =
> ; List of times at the annealing points for each group
> annealing_time =
> ; Temp. at each annealing point, for each group.
> annealing_temp =
>
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel = yes
> gen_temp = 300
> gen_seed = 1993
>
> ; OPTIONS FOR BONDS
> constraints = h-bonds
> ; Type of constraint algorithm
> constraint-algorithm = Lincs
> ; Do not constrain the start configuration
> unconstrained-start = no
> ; Use successive overrelaxation to reduce the number of shake iterations
> Shake-SOR = no
> ; Relative tolerance of shake
> shake-tol = 1e-04
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 4
> ; Number of iterations in the final step of LINCS. 1 is fine for
> ; normal simulations, but use 2 to conserve energy in NVE runs.
> ; For energy minimization with constraints it should be 4 to 8.
> lincs-iter = 1
> ; Lincs will write a warning to the stderr if in one step a bond
> ; rotates over more degrees than
> lincs-warnangle = 30
> ; Convert harmonic bonds to morse potentials
> morse = no
>
> ; ENERGY GROUP EXCLUSIONS
> ; Pairs of energy groups for which all non-bonded interactions are excluded
> energygrp_excl =
>
> ; NMR refinement stuff
> ; Distance restraints type: No, Simple or Ensemble
> disre = No
> ; Force weighting of pairs in one distance restraint: Conservative or Equal
> disre-weighting = Conservative
> ; Use sqrt of the time averaged times the instantaneous violation
> disre-mixed = no
> disre-fc = 1000
> disre-tau = 0
> ; Output frequency for pair distances to energy file
> nstdisreout = 100
> ; Orientation restraints: No or Yes
> orire = no
> ; Orientation restraints force constant and tau for time averaging
> orire-fc = 0
> orire-tau = 0
> orire-fitgrp =
> ; Output frequency for trace(SD) to energy file
> nstorireout = 100
> ; Dihedral angle restraints: No, Simple or Ensemble
> dihre = No
> dihre-fc = 1000
> dihre-tau = 0
> ; Output frequency for dihedral values to energy file
> nstdihreout = 100
>
> ; Free energy control stuff
> free-energy = no
> init-lambda = 0
> delta-lambda = 0
> sc-alpha = 0
> sc-sigma = 0.3
>
> ; Non-equilibrium MD stuff
> acc-grps =
> accelerate =
> freezegrps =
> freezedim =
> cos-acceleration = 0
>
> ; Electric fields
> ; Format is number of terms (int) and for all terms an amplitude (real)
> ; and a phase angle (real)
> E-x =
> E-xt =
> E-y =
> E-yt =
> E-z =
> E-zt =
>
> ; User defined thingies
> user1-grps =
> user2-grps =
> userint1 = 0
> userint2 = 0
> userint3 = 0
> userint4 = 0
> userreal1 = 0
> userreal2 = 0
> userreal3 = 0
> userreal4 = 0
>
> LOG FILE
> Log file opened on Wed Jun 22 09:00:54 2016
> Host: compute-0-2.local pid: 9075 nodeid: 0 nnodes: 1
> The Gromacs distribution was built Tue Nov 27 15:50:05 PST 2012 by
> root at centos-6-3.localdomain (Linux 2.6.32-279.14.1.el6.x86_64 x86_64)
>
>
> :-) G R O M A C S (-:
>
> Grunge ROck MAChoS
>
> :-) VERSION 4.5.4 (-:
>
> Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
> Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
> Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
> Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
> Michael Shirts, Alfons Sijbers, Peter Tieleman,
>
> Berk Hess, David van der Spoel, and Erik Lindahl.
>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2010, The GROMACS development team at
> Uppsala University & The Royal Institute of Technology, Sweden.
> check out http://www.gromacs.org for more information.
>
> This program is free software; you can redistribute it and/or
> modify it under the terms of the GNU General Public License
> as published by the Free Software Foundation; either version 2
> of the License, or (at your option) any later version.
>
> :-) mdrun (-:
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
> GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
> molecular simulation
> J. Chem. Theory Comput. 4 (2008) pp. 435-447
> -------- -------- --- Thank You --- -------- --------
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
> Berendsen
> GROMACS: Fast, Flexible and Free
> J. Comp. Chem. 26 (2005) pp. 1701-1719
> -------- -------- --- Thank You --- -------- --------
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> E. Lindahl and B. Hess and D. van der Spoel
> GROMACS 3.0: A package for molecular simulation and trajectory analysis
> J. Mol. Mod. 7 (2001) pp. 306-317
> -------- -------- --- Thank You --- -------- --------
>
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> H. J. C. Berendsen, D. van der Spoel and R. van Drunen
> GROMACS: A message-passing parallel molecular dynamics implementation
> Comp. Phys. Comm. 91 (1995) pp. 43-56
> -------- -------- --- Thank You --- -------- --------
>
> Input Parameters:
> integrator = md
> nsteps = 1000000
> init_step = 0
> ns_type = Grid
> nstlist = 20
> ndelta = 2
> nstcomm = 20
> comm_mode = Linear
> nstlog = 50
> nstxout = 100
> nstvout = 100
> nstfout = 0
> nstcalcenergy = 20
> nstenergy = 60
> nstxtcout = 1
> init_t = 0
> delta_t = 0.0001
> xtcprec = 1000
> nkx = 25
> nky = 25
> nkz = 25
> pme_order = 4
> ewald_rtol = 1e-05
> ewald_geometry = 0
> epsilon_surface = 0
> optimize_fft = FALSE
> ePBC = xyz
> bPeriodicMols = FALSE
> bContinuation = FALSE
> bShakeSOR = FALSE
> etc = V-rescale
> nsttcouple = 20
> epc = Berendsen
> epctype = Isotropic
> nstpcouple = 20
> tau_p = 1
> 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 = 1.2
> rlistlong = 1.2
> rtpi = 0.05
> coulombtype = PME
> rcoulomb_switch = 0
> rcoulomb = 1.2
> vdwtype = Cut-off
> rvdw_switch = 0
> rvdw = 1.2
> epsilon_r = 1
> epsilon_rf = 1
> tabext = 1
> implicit_solvent = No
> gb_algorithm = Still
> gb_epsilon_solvent = 80
> nstgbradii = 1
> rgbradii = 2
> 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 = 100
> niter = 20
> fc_stepsize = 0
> nstcgsteep = 1000
> nbfgscorr = 10
> ConstAlg = Lincs
> 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: 11751
> ref_t: 300
> tau_t: 0.1
> anneal: No
> ann_npoints: 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.
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen
> A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
>
> Will do ordinary reciprocal space Ewald sum.
> Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
> Cut-off's: NS: 1.2 Coulomb: 1.2 LJ: 1.2
> Long Range LJ corr.: <C6> 3.3273e-04
> System total charge: -0.000
> Generated table with 1100 data points for Ewald.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for LJ6.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for LJ12.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for 1-4 COUL.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for 1-4 LJ6.
> Tabscale = 500 points/nm
> Generated table with 1100 data points for 1-4 LJ12.
> Tabscale = 500 points/nm
>
> Enabling SPC-like water optimization for 1359 molecules.
>
> Configuring nonbonded kernels...
> Configuring standard C nonbonded kernels...
> Testing x86_64 SSE2 support... present.
>
>
> Removing pbc first time
>
> Initializing LINear Constraint Solver
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
> LINCS: A Linear Constraint Solver for molecular simulations
> J. Comp. Chem. 18 (1997) pp. 1463-1472
> -------- -------- --- Thank You --- -------- --------
>
> The number of constraints is 900
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> S. Miyamoto and P. A. Kollman
> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
> Water Models
> J. Comp. Chem. 13 (1992) pp. 952-962
> -------- -------- --- Thank You --- -------- --------
>
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest
>
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> G. Bussi, D. Donadio and M. Parrinello
> Canonical sampling through velocity rescaling
> J. Chem. Phys. 126 (2007) pp. 014101
> -------- -------- --- Thank You --- -------- --------
>
> SIMULATION RECAP
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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