[gmx-users] Re: NS in PME
David Mobley
dmobley at gmail.com
Tue Apr 11 17:07:50 CEST 2006
Janne,
You may want to look on the GROMACS developers list for a lot of
recent discussion relating to energy conservation. It is a fairly
complicated issue. http://www.gromacs.org/pipermail/gmx-developers/
David
On 4/11/06, Janne Hirvi <janne.hirvi at joensuu.fi> wrote:
> Thanks for your response David!
>
> I tried to simulate bulk water (1372 SPC/E molecules) with your parameters and
> observed same kind of problems with energy conservation as with my earlier
> parameters (rlist=rvdw=rcoulomb=1.2 & nstlist=10). In single precision NVE
> simulation (500ps) drift in total energy was +1828.88kJ/mol with your
> parameters and +1861.13kJ/mol with mine. So I am little bit confused and I
> still have couple of questions:
>
> 1) Are this large drifts normal or have I done something stupid? I mean have
> you
> observed this kind of artifacts as well? Atleast from the next mail I would
> think that better energy conservation should be achieved with your parameters?
>
> http://www.gromacs.org/pipermail/gmx-users/2002-December/003510.html
>
> 2) I still dont understand why parameter combination rlist>rcoulomb with PME
> conserves total energy almost completely, but however I should use parameters
> so
> that rlist=rcoulomb. Can you comment on this because Berk may have noted your
> request or then he have had no time to do that? Or is it so trivial that I
> should find explanation from some trivial text book?
>
>
> Thanks,
>
> Janne
>
>
>
> > Janne Hirvi wrote:
> > > Hello David!
> > >
> > > I read your interesting new article "The Origin of Layer Structure
> > Artifacts in
> > > Simulations of Liquid Water" and I would like to know especially what kind
> > of
> > > NS parameters you have used in the simulations with PME and are the
> > following
> > > parameters correct otherwise?
> > >
> > > dt=0.002
> > > nstlist=5
> > > rlist=?
> > > coulombtype=PME
> > > rcoulomb=0.9
> > > vdwtype=cut-off
> > > rvdw=?
> > I'm attaching my mdp file.
> >
> > We have just disabled the option to have rlist != rcoulomb with PME.
> >
> > >
> > > I am interested especially about the rlist parameter because there seems to
> > be
> > > some energy conservation problems in my water simulations. At least I
> > couldn't
> > > achieve energy conservation with single precision complilation and with
> > > double precision compilation energy is conserved only when switch(shift?)
> > > function is used for vdw interactions (rlist>rvdw>rvdw_switch) and PME for
> > > coulombic interactions (rlist>rcoulomb). If rlist is equal to rcoulomb I
> > need
> > > to update NS list at every time step but with preceding parameters energy
> > is
> > > conserved even when nstlist=10.
> > >
> > > So should I use rlist>rcoulomb with PME when nstlist>1 to take into
> > account
> > > movement of atoms/molecules(charge groups) near the real space cut-off
> > limit
> > > (rcoulomb) or is there something I don't understand? Atleast from the
> > manual
> > > someone could get the picture that rlist should be equal to rcoulomb and
> > there
> > > are also different kind of opinions on mailing list?
> >
> > Maybe Berk can comment?
> >
> > >
> > >
> > > Thanks for any comments in advance!
> > >
> > > Janne
> > >
> > >
> >
> ------------------------------------------------------------------------------
> > > Janne Hirvi, MSc(Physical Chemistry), Researcher
> > > University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu,
> > FI
> > > Tel: +358 13 2514544 & +358 50 3474223
> > > E-mail: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
> > >
> >
> ------------------------------------------------------------------------------
> > > _______________________________________________
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> >
> >
> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > -------------- next part --------------
> > ;
> > ; File 'mdout.mdp' was generated
> > ; By user: spoel (291)
> > ; On host: matisse
> > ; At date: Sun Aug 11 22:20:40 2002
> > ;
> >
> > ; VARIOUS PREPROCESSING OPTIONS =
> > title =
> > cpp = /lib/cpp
> >
> > ; RUN CONTROL PARAMETERS =
> > integrator = md
> > ; start time and timestep in ps =
> > tinit = 0
> > dt = 0.002
> > nsteps = 1000000
> > ; 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 =
> > bd-temp = 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
> >
> > ; 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 = 1000
> > nstenergy = 100
> > ; Output frequency and precision for xtc file =
> > nstxtcout = 250
> > 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 = 5
> > ; ns algorithm (simple or grid) =
> > ns-type = Grid
> > ; Periodic boundary conditions: xyz or no =
> > pbc = xyz
> > ; nblist cut-off =
> > domain-decomposition = no
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW =
> > ; Method for doing electrostatics =
> > coulombtype = PME
> > rcoulomb-switch = 0
> > ; 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
> > ; Apply long range dispersion corrections for Energy and Pressure =
> > DispCorr = Ener
> > ; Spacing for the PME/PPPM FFT grid =
> > fourierspacing = 0.12
> > ; 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
> >
> > ; OPTIONS FOR WEAK COUPLING ALGORITHMS =
> > ; Temperature coupling =
> > tcoupl = Berendsen
> > ; Groups to couple separately =
> > tc-grps = System
> > ; Time constant (ps) and reference temperature (K) =
> > tau-t = 0.1
> > ref-t = 298.15
> > ; Pressure coupling =
> > Pcoupl = Berendsen
> > Pcoupltype = Isotropic
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar) =
> > tau-p = 1.0
> > compressibility = 5e-5
> > ref-p = 1
> >
> > ; SIMULATED ANNEALING CONTROL =
> > annealing = no
> > ; Time at which temperature should be zero (ps) =
> > zero-temp_time = 0
> >
> > ; GENERATE VELOCITIES FOR STARTUP RUN =
> > gen-vel = yes
> > gen-temp = 300
> > gen-seed = 173529
> >
> > ; OPTIONS FOR BONDS =
> > constraints = none
> > ; Type of constraint algorithm =
> > constraint-algorithm = shake
> > ; 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
> > ; 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
> >
> > ; 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
> > rlist = 0.9
> > rcoulomb = 0.9
> > rvdw = 0.9
> _______________________________________________
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> http://www.gromacs.org/mailman/listinfo/gmx-users
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