[gmx-developers] Drift in Conserved-Energy with Nose-Hoover thermostat
Mark Abraham
mark.j.abraham at gmail.com
Wed Jul 15 19:01:50 CEST 2015
Hi,
Yes, that's a problem long fixed, and several orders of magnitude larger.
Mark
On Wed, Jul 15, 2015 at 6:16 PM Bernhard <b.reuter at uni-kassel.de> wrote:
> I remember some research article http://dx.doi.org/10.1063/1.2431176 (or
>
> https://www.deshawresearch.com/publications/A%20common,%20avoidable%20source%20of%20error%20in%20molecular%20dynamics%20integrators.pdf
> )
> from 2006 which showed a comparable linear energy drift for single
> precision GROMACS 3.3.1 due to not optimal calculation of the velocity
> of constrained particels.
> But this issue should be solved in version 4.6.7?
>
> Best,
> Bernhard
>
> Am 15/07/15 um 18:04 schrieb Bernhard:
> > Indeed seems so... unfortunately I have no clue about the cause.
> > Maybe the head of the .log file is of some use?
> >
> > Log file opened on Wed Jul 1 17:33:48 2015
> > Host: theo2-pc20 pid: 15411 nodeid: 0 nnodes: 1
> > Gromacs version: VERSION 4.6.7
> > Precision: single
> > Memory model: 64 bit
> > MPI library: thread_mpi
> > OpenMP support: enabled
> > GPU support: disabled
> > invsqrt routine: gmx_software_invsqrt(x)
> > CPU acceleration: AVX_256
> > FFT library: fftw-3.3.2-sse2
> > Large file support: enabled
> > RDTSCP usage: enabled
> > Built on: Di 16. Jun 15:38:40 CEST 2015
> > Built by: berni at theo2-pc20 [CMAKE]
> > Build OS/arch: Linux 3.13.0-43-generic x86_64
> > Build CPU vendor: GenuineIntel
> > Build CPU brand: Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz
> > Build CPU family: 6 Model: 62 Stepping: 4
> > Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm
> > mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp
> > sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > C compiler: /usr/bin/cc GNU cc (Ubuntu 4.8.2-19ubuntu1) 4.8.2
> > C compiler flags: -mavx -Wextra -Wno-missing-field-initializers
> > -Wno-sign-compare -Wall -Wno-unused -Wunused-value
> > -Wno-unused-parameter -Wno-array-bounds -Wno-maybe-uninitialized
> > -Wno-strict-overflow -fomit-frame-pointer -funroll-all-loops
> > -fexcess-precision=fast -O3 -DNDEBUG
> >
> >
> > :-) G R O M A C S (-:
> >
> > GROwing Monsters And Cloning Shrimps
> >
> > :-) VERSION 4.6.7 (-:
> >
> > Contributions from Mark Abraham, Emile Apol, Rossen Apostolov,
> > Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar,
> > Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph
> > Junghans,
> > Peter Kasson, Carsten Kutzner, 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) 2001-2012,2013, 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 Lesser General Public License
> > as published by the Free Software Foundation; either version 2.1
> > 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 = 10000000
> > init-step = 0
> > cutoff-scheme = Verlet
> > ns_type = Grid
> > nstlist = 10
> > ndelta = 2
> > nstcomm = 100
> > comm-mode = Linear
> > nstlog = 5000
> > nstxout = 5000
> > nstvout = 5000
> > nstfout = 0
> > nstcalcenergy = 100
> > nstenergy = 1000
> > nstxtcout = 1000
> > init-t = 0
> > delta-t = 0.001
> > xtcprec = 1000
> > fourierspacing = 0.12
> > nkx = 60
> > nky = 60
> > nkz = 60
> > 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 = Nose-Hoover
> > bPrintNHChains = FALSE
> > nsttcouple = 10
> > epc = No
> > epctype = Isotropic
> > nstpcouple = -1
> > tau-p = 1
> > ref-p (3x3):
> > ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > compress (3x3):
> > compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > 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
> > verlet-buffer-drift = 0.005
> > rlist = 1
> > rlistlong = 1
> > nstcalclr = 10
> > rtpi = 0.05
> > coulombtype = PME
> > coulomb-modifier = Potential-shift
> > rcoulomb-switch = 0
> > rcoulomb = 1
> > vdwtype = Cut-off
> > vdw-modifier = Potential-shift
> > rvdw-switch = 0
> > rvdw = 1
> > epsilon-r = 1
> > epsilon-rf = inf
> > 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
> > bSimTemp = FALSE
> > free-energy = no
> > 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
> > rotation = FALSE
> > 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 = 0
> > em-stepsize = 0.01
> > em-tol = 10
> > 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}
> > adress = FALSE
> > userint1 = 0
> > userint2 = 0
> > userint3 = 0
> > userint4 = 0
> > userreal1 = 0
> > userreal2 = 0
> > userreal3 = 0
> > userreal4 = 0
> > grpopts:
> > nrdf: 1501.9 44334.1
> > ref-t: 300 300
> > tau-t: 2.5 2.5
> > 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
> > Using 1 MPI thread
> > Using 12 OpenMP threads
> >
> > Detecting CPU-specific acceleration.
> > Present hardware specification:
> > Vendor: GenuineIntel
> > Brand: Intel(R) Core(TM) i7-4930K CPU @ 3.40GHz
> > Family: 6 Model: 62 Stepping: 4
> > Features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm mmx msr
> > nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2
> > sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > Acceleration most likely to fit this hardware: AVX_256
> > Acceleration selected at GROMACS compile time: AVX_256
> >
> > Will do PME sum in reciprocal space.
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > U. Essmann, L. Perera, 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 0.320163 nm for Ewald
> > Cut-off's: NS: 1 Coulomb: 1 LJ: 1
> > Long Range LJ corr.: <C6> 2.8855e-04
> > System total charge: 0.000
> > Generated table with 1000 data points for Ewald.
> > Tabscale = 500 points/nm
> > Generated table with 1000 data points for LJ6.
> > Tabscale = 500 points/nm
> > Generated table with 1000 data points for LJ12.
> > Tabscale = 500 points/nm
> > Generated table with 1000 data points for 1-4 COUL.
> > Tabscale = 500 points/nm
> > Generated table with 1000 data points for 1-4 LJ6.
> > Tabscale = 500 points/nm
> > Generated table with 1000 data points for 1-4 LJ12.
> > Tabscale = 500 points/nm
> >
> > Using AVX-256 4x4 non-bonded kernels
> >
> > Using Lorentz-Berthelot Lennard-Jones combination rule
> >
> > Potential shift: LJ r^-12: 1.000 r^-6 1.000, Ewald 1.000e-05
> > Initialized non-bonded Ewald correction tables, spacing: 6.60e-04
> > size: 3033
> >
> > Pinning threads with an auto-selected logical core stride of 1
> >
> > 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 292
> >
> > ++++ 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
> > There are: 22765 Atoms
> > Initial temperature: 299.915 K
> >
> >
> > Am 15/07/15 um 17:57 schrieb Shirts, Michael R. (mrs5pt):
> >>> There I also got a linear drift (but smaller) of 0.78 kJ/mol/ps
> >>> (3.436*10^-5 kJ/mol/ps per atom).
> >>> For comparison reasons I also did a NVT Nose-Hoover Simulation with
> >>> manually set rlist=1.012nm: There I got a comparable linear drift of
> >>> 0.67
> >>> kJ/mol/ps (2.94*10^-5 kJ/mol/ps per atom). So no differences between
> >>> NVE
> >>> and NVT so far in my opinion...
> >>
> >> So sounds like the conserved quantity drift with NVT is not due to
> >> NH, but
> >> due to something else with the underlying dynamics.
> >>
> >> Best,
> >> ~~~~~~~~~~~~
> >> Michael Shirts
> >> Associate Professor
> >> Department of Chemical Engineering
> >> University of Virginia
> >> michael.shirts at virginia.edu
> >> (434) 243-1821
> >>
> >>
> >>
> >> On 7/15/15, 11:41 AM, "Bernhard" <b.reuter at uni-kassel.de> wrote:
> >>
> >>> I mean a drift of the total energy in NVE - while with Nose-Hoover the
> >>> drift is in the Conserved-Energy quantity of g_energy (the total energy
> >>> shows no drift with Noose-Hoover...).
> >>>
> >>> Am 15/07/15 um 17:38 schrieb Bernhard:
> >>>> I also did a NVE simulation with the same parameters, system and
> >>>> starting conditions but with manually set rlist=1.012nm (since
> >>>> verlet-buffer-drift doesnt work in NVE):
> >>>> There I also got a linear drift (but smaller) of 0.78 kJ/mol/ps
> >>>> (3.436*10^-5 kJ/mol/ps per atom).
> >>>> For comparison reasons I also did a NVT Nose-Hoover Simulation with
> >>>> manually set rlist=1.012nm:
> >>>> There I got a comparable linear drift of 0.67 kJ/mol/ps (2.94*10^-5
> >>>> kJ/mol/ps per atom).
> >>>> So no differences between NVE and NVT so far in my opinion...
> >>>>
> >>>>
> >>>>
> >>>> Best,
> >>>> Bernhard
> >>>>
> >>>> Am 15/07/15 um 17:10 schrieb Shirts, Michael R. (mrs5pt):
> >>>>> The conserved quantity in nose-hoover is not quite as good as the
> >>>>> conserved energy, which should have no drift at all. For NH, the
> >>>>> conserved quantity should drift as a random Gaussian process with
> >>>>> mean
> >>>>> zero (i.e. go with sqrt(N)). It shouldn't be drifting linearly.
> >>>>>
> >>>>> I would check to see if your system conserved energy when run with
> >>>>> NVE
> >>>>> (use the endpoint of the NPT simulation). It's easier to diagnose
> >>>>> any
> >>>>> problems with an NVE simulation, which should have virtually no
> >>>>> drift, vs
> >>>>> a NVT simulation, which has random noise drift. Odds are, if
> >>>>> there is
> >>>>> a
> >>>>> problem with the NVT simulation, it will also show up in the NVE
> >>>>> simulation if only the thermostat is removed.
> >>>>>
> >>>>> Also, consider looking at
> >>>>> http://pubs.acs.org/doi/abs/10.1021/ct300688p
> >>>>> for tests of whether the ensemble generated is correct.
> >>>>>
> >>>>> Best,
> >>>>> ~~~~~~~~~~~~
> >>>>> Michael Shirts
> >>>>> Associate Professor
> >>>>> Department of Chemical Engineering
> >>>>> University of Virginia
> >>>>> michael.shirts at virginia.edu
> >>>>> (434) 243-1821
> >>>>>
> >>>>>
> >>>>>
> >>>>> On 7/15/15, 10:58 AM, "Bernhard" <b.reuter at uni-kassel.de> wrote:
> >>>>>
> >>>>>> Dear Gromacs Users and Developers,
> >>>>>>
> >>>>>> I have a problem regarding energy conservation in my 10ns NVT
> >>>>>> protein+water+ions (22765 atoms) production (minimization and
> >>>>>> equilibration for more than 15ns was carried out in NPT before)
> >>>>>> simulations using a Nose-Hoover thermostat (tau=2.5ps).
> >>>>>> On first glance everything looks fine - the potential, kinetic and
> >>>>>> total
> >>>>>> energy are nearly perfectly constant (with normal fluctuations) -
> >>>>>> but
> >>>>>> when I checked the "Conserved-Energy" quantity that g_energy
> >>>>>> outputs I
> >>>>>> had to recognize a significant (nearly perfectly) linear downward
> >>>>>> drift
> >>>>>> of this "to-be-conserved" quantity of around 1.7 kJ/mol/ps
> >>>>>> (7.48*10^-5
> >>>>>> kJ/mol/ps per atom).
> >>>>>> This appears somehow disturbing to me since I would expect that this
> >>>>>> Conserved-Energy is the conserved energy of the extended Nose-Hoover
> >>>>>> Hamiltonian - which should by definition be conserved.
> >>>>>>
> >>>>>> If it would be a drift caused by normal round-off error due to
> >>>>>> single
> >>>>>> precision I would expect it to grow with Sqrt(N) and not with N
> >>>>>> (linear)
> >>>>>> (N=number of steps).
> >>>>>> So I would like to know if this is a normal behaviour and also what
> >>>>>> could cause this (buffer size, precision, constraints etc)?
> >>>>>> Also I would like to know, if I am correct with my guess that the
> >>>>>> "Conserved-Energy" quantity is in this case the energy of the
> >>>>>> extended
> >>>>>> Nose-Hoover Hamiltonian?
> >>>>>> The .mdp file is atatched (don't be confused about rlist=1 -
> >>>>>> since Im
> >>>>>> using the Verlet-scheme the verlet-buffer-drift option should be by
> >>>>>> default active and determine the rlist value (Verlet buffer-size)
> >>>>>> automatically).
> >>>>>>
> >>>>>> Best regards,
> >>>>>> Bernhard
> >>>>>>
> >>>>>> ; Run parameters
> >>>>>> integrator = md ; leap-frog integrator
> >>>>>> nsteps = 10000000 ; 10000 ps = 10 ns
> >>>>>> dt = 0.001 ; 1 fs
> >>>>>> ; Output control
> >>>>>> nstxout = 5000 ; save coordinates every ps
> >>>>>> nstvout = 5000 ; save velocities every ps
> >>>>>> nstxtcout = 1000 ; xtc compressed trajectory output
> >>>>>> every ps
> >>>>>> nstenergy = 1000 ; save energies every ps
> >>>>>> nstlog = 5000 ; update log file every ps
> >>>>>> ; Bond parameters
> >>>>>> continuation = yes ; continue from NPT
> >>>>>> constraint_algorithm = lincs ; holonomic constraints
> >>>>>> constraints = h-bonds ; all bonds (even heavy atom-H bonds)
> >>>>>> constrained
> >>>>>> lincs_iter = 1 ; accuracy of LINCS
> >>>>>> lincs_order = 4 ; also related to accuracy
> >>>>>> ; Neighborsearching
> >>>>>> cutoff-scheme = Verlet ; Verlet cutoff-scheme instead of
> >>>>>> group-scheme (no charge-groups used)
> >>>>>> ns_type = grid ; search neighboring grid cells
> >>>>>> nstlist = 10 ; 10 fs
> >>>>>> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> >>>>>> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> >>>>>> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> >>>>>> ; Electrostatics
> >>>>>> coulombtype = PME ; Particle Mesh Ewald for long-range
> >>>>>> electrostatics
> >>>>>> pme_order = 4 ; cubic interpolation
> >>>>>> fourierspacing = 0.12 ; grid spacing for FFT
> >>>>>> ; Temperature coupling is on
> >>>>>> tcoupl = nose-hoover ; modified Berendsen thermostat
> >>>>>> tc-grps = Protein Non-Protein ; two coupling groups - more
> >>>>>> accurate
> >>>>>> tau_t = 2.5 2.5 ; time constant, in ps
> >>>>>> ref_t = 300 300 ; reference temperature, one for each
> >>>>>> group, in K
> >>>>>> ; Pressure coupling is off
> >>>>>> pcoupl = no ; no pressure coupling in NVT
> >>>>>> ; Periodic boundary conditions
> >>>>>> pbc = xyz ; 3-D PBC
> >>>>>> ; Dispersion correction
> >>>>>> DispCorr = EnerPres ; account for cut-off vdW scheme
> >>>>>> ; Velocity generation
> >>>>>> gen_vel = no ; don¹t assign velocities from Maxwell
> >>>>>> distribution
> >>>>>>
> >>>>>> --
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> >>>>>>
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