[gmx-developers] Drift in Conserved-Energy with Nose-Hoover thermostat
Mark Abraham
mark.j.abraham at gmail.com
Wed Jul 15 18:14:52 CEST 2015
Hi,
This looks approximately normal for constrained dynamics of systems with
water. See e.g. fig 8 of http://dx.doi.org/10.1016/j.cpc.2013.06.003
Mark
On Wed, Jul 15, 2015 at 5:57 PM Bernhard <b.reuter at uni-kassel.de> wrote:
> I now also tried with bigger manual rlist values of 1.02 and 1.05: This
> doesnt help - the drift of the conserved energy with Nose-Hoover gets
> even bigger: -1,8 kJ/mol/ps (7.9*10^-5 kJ/mol/ps per atom) and -2.62
> kJ/mol/ps (1.15*10^-4 kJ/mol/ps per atom).
>
> Am 15/07/15 um 17:41 schrieb Bernhard:
> > 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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> >>
> >
>
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