[gmx-users] Re: NS in PME
David van der Spoel
spoel at xray.bmc.uu.se
Tue Apr 11 15:07:10 CEST 2006
Janne Hirvi 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?
>
this is not trivial. you may want to decrease ewald_rtol to 1e-6 and use
a shift for the vanderwaals interactions.
>
> 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
> Please don't post (un)subscribe requests to the list. Use the
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> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
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