[gmx-developers] md-vv and v-rescale thermostat?
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Sep 4 10:58:57 CEST 2012
On 4/09/2012 3:10 PM, Shirts, Michael (mrs5pt) wrote:
> With 4.6, I get a system that starts with the same incorrect temperature,
> but rapidly regresses to the correct temperature controlled temperature.
Yes, that should happen with gen_vel = yes and continuation = yes. If I
turn continuation = no (which I should have been doing, sorry) then I
get a sensible step 0 and then similar over-heating (with md = vv on
release-4-5-patches), which seems to confirm the bug:
Constraining the starting coordinates (step 0)
RMS relative constraint deviation after constraining: 0.00e+00
Initial temperature: 287.379 K
Started mdrun on node 0 Tue Sep 4 18:01:02 2012
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
1.56860e+04 -2.52945e+02 -3.28461e+04 -3.72301e+03 -2.11360e+04
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
6.44783e+03 -1.46882e+04 -1.46882e+04 2.87379e+02 -1.54019e+02
Pressure (bar)
2.87991e+04
Step Time Lambda
500 1.00000 0.00000
Energies (kJ/mol)
LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. Potential
8.73207e+03 -2.52945e+02 -1.74964e+04 -3.23860e+03 -1.22559e+04
Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar)
4.15181e+04 2.92622e+04 2.42426e+04 1.85045e+03 -1.54019e+02
Pressure (bar)
3.08189e+04
(Hmmm, also this suggests grompp should be issuing a warning or note
about gen_vel = yes and continuation = yes. Probably a warning, since we
can't presume which mistake the user made, since you can't generate
velocities and do continuation. And goes in 4.6 since we don't want to
affect the behaviour of grompp which is not technically buggy.)
> It starts with the wrong temperature because continuation is set to yes, and
> it's likely a starting point from a leapfrog simulation, correct? There's a
> mismatch between storing the half step and full step velocities between the
> two programs, so that's pretty much expected behavior. I don't think
> there's a way to avoid that, because it would require knowing what that LAST
> simulation did, which can't be done.
Each is starting from the same gen_vel = yes velocity vector. Obviously,
the interpretation of v differs between integrators, and so will the
trajectory, but both should equilibrate - and should do so regardless of
continuation=yes, despite the erroneous T spike that causes. My new
observations above seem to confirm the integrator problem.
> So, it looks like a bug that has been fixed. I will take a look at see
> exactly where it was fixed to propose a bug fix for 4.5, but it's a little
> too late tonight to mange that . . .
OK, thanks.
Mark
>
> 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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