[gmx-developers] md-vv and v-rescale thermostat?
Shirts, Michael (mrs5pt)
mrs5pt at eservices.virginia.edu
Mon Sep 3 15:52:36 CEST 2012
Strange. I've tested this before. Though perhaps I only tested in 4.6
pre-release, and a fix needs to be regressed. . . I'll look at this when I
get a chance today.
Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Mon, 3 Sep 2012 23:43:05 +1000
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: [gmx-developers] md-vv and v-rescale thermostat?
>
> Hi,
>
> I tried the md-vv integrator in release-4-5-patches (2859895) in concert
> with the v-rescale (Bussi) thermostat and found some weird heating
> behaviour on a 900-TIP3P system that was fine with the md integrator.
> (.mdp file at end of email) Michael (or anybody else) is/was this
> thermostat known to work with md-vv?
>
> With md-vv:
>
> Step Time Lambda
> 0 0.00000 0.00000
>
> Energies (kJ/mol)
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
> 1.56788e+04 -2.52945e+02 -3.58017e+04 -3.73679e+03 -2.41127e+04
> Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
> 9.86312e+03 -1.42495e+04 -1.42495e+04 4.39597e+02 -1.54019e+02
> Pressure (bar)
> -5.69569e+04
>
>
> Step Time Lambda
> 500 1.00000 0.00000
>
> Energies (kJ/mol)
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
> 8.23626e+03 -2.52945e+02 -1.74349e+04 -3.27515e+03 -1.27267e+04
> Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
> 4.19512e+04 2.92245e+04 2.45247e+04 1.86976e+03 -1.54019e+02
> Pressure (bar)
> 2.97051e+04
>
> <snip>
>
> Step Time Lambda
> 500000 1000.00000 0.00000
>
> Writing checkpoint, step 500000 at Mon Sep 3 23:15:57 2012
>
>
> Energies (kJ/mol)
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
> 1.01917e+04 -2.52945e+02 -1.51940e+04 -3.02693e+03 -8.28214e+03
> Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
> 5.17784e+04 4.34963e+04 4.79009e+04 2.30775e+03 -1.54019e+02
> Pressure (bar)
> 3.82536e+04
>
> <====== ############### ==>
> <==== A V E R A G E S ====>
> <== ############### ======>
>
> Statistics over 500001 steps using 50001 frames
>
> Energies (kJ/mol)
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
> 9.71441e+03 -2.52945e+02 -1.51389e+04 -3.03171e+03 -8.70917e+03
> Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
> 5.25444e+04 4.38352e+04 4.10799e+04 2.34189e+03 -1.54019e+02
> Pressure (bar)
> 3.73202e+04
>
> Obviously this is heating massively at the start and the thermostat is
> totally failing to deal with it. With integrator md:
>
> Step Time Lambda
>
> 0 0.00000 0.00000
>
> Energies (kJ/mol)
>
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
>
> 1.56788e+04 -2.52945e+02 -3.58017e+04 -3.73679e+03 -2.41127e+04
>
> Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
>
> 1.30540e+04 -1.10587e+04 -1.10587e+04 5.81814e+02 -1.54019e+02
>
> Pressure (bar)
>
> -1.29542e+04
>
> Step Time Lambda
>
> 500 1.00000 0.00000
>
> Energies (kJ/mol)
>
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
>
> 4.57027e+03 -2.52945e+02 -3.01897e+04 -4.38326e+03 -3.02556e+04
>
> Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
>
> 1.07502e+04 -1.95054e+04 -1.39359e+04 4.79135e+02 -1.54019e+02
>
> Pressure (bar)
>
> 3.29939e+03
>
> <snip>
>
> Step Time Lambda
>
> 500000 1000.00000 0.00000
>
> Writing checkpoint, step 500000 at Wed Aug 29 01:54:51 2012
>
> Energies (kJ/mol)
>
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
>
> 5.72530e+03 -2.52945e+02 -3.72877e+04 -4.50918e+03 -3.63246e+04
>
> Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
>
> 6.59347e+03 -2.97311e+04 -1.25805e+04 2.93870e+02 -1.54019e+02
>
> Pressure (bar)
>
> -1.82664e+02
>
> <====== ############### ==>
>
> <==== A V E R A G E S ====>
>
> <== ############### ======>
>
> Statistics over 500001 steps using 50001 frames
>
> Energies (kJ/mol)
>
> LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
>
> 5.74509e+03 -2.52945e+02 -3.72807e+04 -4.52328e+03 -3.63118e+04
>
> Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
>
> 6.58722e+03 -2.97246e+04 -1.32539e+04 2.93591e+02 -1.54019e+02
>
> Pressure (bar)
>
> -4.77602e+01
>
> This looks fine.
>
> Mark
>
> ; VARIOUS PREPROCESSING OPTIONS
> ; Preprocessor information: use cpp syntax.
> ; e.g.: -I/home/joe/doe -I/home/mary/roe
> include =
> ; e.g.: -DI_Want_Cookies -DMe_Too
> ;define = -DPOSRES
>
> ; RUN CONTROL PARAMETERS
> integrator = md-vv
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.002
> nsteps = 500000
> ; For exact run continuation or redoing part of a run
> init_step = 0
> ; Part index is updated automatically on checkpointing (keeps files separate)
> simulation_part = 1
> ; mode for center of mass motion removal
> ; energy calculation and T/P-coupling frequency
> comm-mode = linear
> ; number of steps for center of mass motion removal
> nstcomm = 10
> ; group(s) for center of mass motion removal
> comm-grps =
>
> ; LANGEVIN DYNAMICS OPTIONS
> ; Friction coefficient (amu/ps) and random seed
> bd-fric = 91
> 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 (ps^2) for minimization of flexible constraints
> fcstep = 0
> ; Frequency of steepest descents steps when doing CG
> nstcgsteep = 1000
> nbfgscorr = 10
>
> ; TEST PARTICLE INSERTION OPTIONS
> rtpi = 0.05
>
> ; OUTPUT CONTROL OPTIONS
> ; Output frequency for coords (x), velocities (v) and forces (f)
> nstxout = 0
> nstvout = 0
> nstfout = 0
> ; Output frequency for energies to log file and energy file
> nstlog = 500
> nstenergy = 500
> ;nstcalcenergy = 1
> ; Output frequency and precision for xtc file
> nstxtcout = 0
> 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 = System
> ; Selection of energy groups
> energygrps =
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 10
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc = xyz
> periodic_molecules = no
> ; nblist cut-off
> rlist = 1.0
> ; long-range cut-off for switched potentials
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = PME
> rcoulomb-switch = 0
> rcoulomb = 1.0
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r = 1
> epsilon_rf = 1
> ; Method for doing Van der Waals
> vdwtype = switch
> ; cut-off lengths
> rvdw_switch = 0.8
> rvdw = 0.9
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = enerpres
> ; Extension of the potential lookup tables beyond the cut-off
> table-extension = 1
> ; Seperate tables between energy group pairs
> energygrp_table =
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.10
> ; 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-6
> ewald_geometry = 3d
> epsilon_surface = 0
> optimize_fft = no
>
> ; IMPLICIT SOLVENT ALGORITHM
> 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 = 1
> ref-t = xxx
> ; Pressure coupling
> Pcoupl = no
> Pcoupltype = Isotropic
> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> tau-p = 1
> compressibility = 4.5e-5
> ref-p = 1.0
> ; Scaling of reference coordinates, No, All or COM
> refcoord_scaling = No
> ; Random seed for Andersen thermostat
> andersen_seed = 815131
>
> ; OPTIONS FOR QMMM calculations
> QMMM = no
> ; Groups treated Quantum Mechanically
> QMMM-grps =
> ; QM method
> QMmethod =
> ; QMMM scheme
> QMMMscheme = normal
> ; QM basisset
> QMbasis =
> ; QM charge
> QMcharge =
> ; QM multiplicity
> QMmult =
> ; Surface Hopping
> SH =
> ; CAS space options
> CASorbitals =
> CASelectrons =
> SAon =
> SAoff =
> SAsteps =
> ; Scale factor for MM charges
> MMChargeScaleFactor = 1
> ; Optimization of QM subsystem
> bOPT =
> bTS =
>
> ; SIMULATED ANNEALING
> ; Type of annealing for each temperature group (no/single/periodic)
> annealing =
> ; 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 = xxx
> gen-seed = 173529
>
> ; OPTIONS FOR BONDS
> constraints = all-bonds
> ; Type of constraint algorithm
> constraint_algorithm = lincs
> ; Do not constrain the start configuration
> continuation = yes
> ; Use successive overrelaxation to reduce the number of shake iterations
> Shake-SOR = no
> ; Relative tolerance of shake
> shake-tol = 0.0001
> ; 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 =
>
> ; WALLS
> ; Number of walls, type, atom types, densities and box-z scale factor for
> Ewald
> nwall = 0
> wall_type = 9-3
> wall_r_linpot = -1
> wall_atomtype =
> wall_density =
> wall_ewald_zfac = 3
>
> ; COM PULLING
> ; Pull type: no, umbrella, constraint or constant_force
> pull = no
>
> ; 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) and S to energy file
> nstorireout = 100
> ; Dihedral angle restraints: No or Yes
> dihre = no
> dihre-fc = 1000
>
> ; Free energy control stuff
> free-energy = no
> init-lambda = 0
> delta-lambda = 0
> foreign_lambda =
> sc-alpha = 0
> sc-power = 0
> sc-sigma = 0.3
> couple-moltype =
> couple-lambda0 = vdw-q
> couple-lambda1 = vdw-q
> couple-intramol = no
>
> ; Non-equilibrium MD stuff
> acc-grps =
> accelerate =
> freezegrps =
> freezedim =
> cos-acceleration = 0
> deform =
>
> ; 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
>
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