[gmx-users] Re: NS in PME
Janne Hirvi
janne.hirvi at joensuu.fi
Tue Apr 11 11:16:22 CEST 2006
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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