[gmx-users] pme problems in gromacs 3.3
David
spoel at xray.bmc.uu.se
Fri Nov 11 21:12:51 CET 2005
On Fri, 2005-11-11 at 14:53 -0500, hseara at netscape.net wrote:
> Thanks David,
>
> Now everything seems to work. But why with order 6 was working in
> 3.2.1 and not now? can you give me a reference where I can learn more
> about what all pme parameter mean? and how to set up them?.
Documentation in the papers.
I seem to recall that a bug was introduced for pme_order != 4 in the 3.3
release, that was fixed recently. What is the problem you are seeing?
Maybe you can file a bugzilla for this and upload a 3.2.1 tpr file that
reproduces the problem.
>
> Thank you, Hector
>
> -----Original Message-----
> From: David <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Fri, 11 Nov 2005 20:21:50 +0100
> Subject: Re: [gmx-users] pme problems in gromacs 3.3
>
> On Fri, 2005-11-11 at 14:07 -0500, hseara at netscape.net wrote:
> > Dear everyone,
> >
> > I'm trying to perform a bilayer simulation with the new gromacs 3.3
> > that works fine with the older version 3.2.1. The problem as far as I
> > know is related to something around "pme". When I turn it off and use
> > cut-off every think works fine. Here is my dun.mdp file when I turn pme
> > on in gromacs 3.3. The same system in gromacs 3.2.1 with this pme file
> > works perfectly. Any help will be apreciated.
>
>
> try pme_order = 4
>
>
> >
> > ;
> > ; File 'mdout.mdp' was generated
> > ; By user: hector (500)
> > ; On host: hectorp
> > ; At date: Tue Nov 8 22:26:19 2005
> > ;
> >
> > ; VARIOUS PREPROCESSING OPTIONS
> > title = MD run on DOPS
> > ; Preprocessor - specify a full path if necessary.
> > cpp = /usr/bin/cpp
> > include =
> > define =
> >
> > ; RUN CONTROL PARAMETERS
> > integrator = md
> > ; Start time and timestep in ps
> > tinit = 0
> > dt = 0.001
> > nsteps = 20000
> > ; For exact run continuation or redoing part of a run
> > init_step = 0
> > ; 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
> > ; Friction coefficient (amu/ps) and random seed
> > bd-fric = 0
> > ld-seed = 1993
> >
> > ; ENERGY MINIMIZATION OPTIONS
> > ; Force tolerance and initial step-size
> > emtol = 50
> > emstep = 0.05
> > ; Max number of iterations in relax_shells
> > niter = 0
> > ; Step size (ps^2) for minimization of flexible constraints
> > fcstep = 0
> > ; Frequency of steepest descents steps when doing CG
> > nstcgsteep = 15000
> > nbfgscorr = 10
> >
> > ; OUTPUT CONTROL OPTIONS
> > ; Output frequency for coords (x), velocities (v) and forces (f)
> > nstxout = 500
> > nstvout = 500
> > nstfout = 0
> > ; Checkpointing helps you continue after crashes
> > nstcheckpoint = 1000
> > ; Output frequency for energies to log file and energy file
> > nstlog = 500
> > nstenergy = 500
> > ; Output frequency and precision for xtc file
> > nstxtcout = 0
> > 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 = 3
> > ; ns algorithm (simple or grid)
> > ns_type = grid
> > ; Periodic boundary conditions: xyz (default), no (vacuum)
> > ; or full (infinite systems only)
> > pbc = xyz
> > ; nblist cut-off
> > rlist = 0.95
> > domain-decomposition = no
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > ; Method for doing electrostatics
> > coulombtype = pme
> > rcoulomb-switch = 0
> > rcoulomb = 0.95
> > ; Relative dielectric constant for the medium and the reaction field
> > epsilon-r = 1
> > epsilon_rf = 1
> > ; Method for doing Van der Waals
> > vdw-type = Cut-off
> > ; cut-off lengths
> > rvdw-switch = 0
> > rvdw = 1.8
> > ; Apply long range dispersion corrections for Energy and Pressure
> > DispCorr = EnerPres
> > ; Extension of the potential lookup tables beyond the cut-off
> > table-extension = 1
> > ; Seperate tables between energy group pairs
> > energygrp_table =
> > ; 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 = 6
> > ewald_rtol = 1e-05
> > ewald_geometry = 3d
> > epsilon_surface = 0
> > optimize_fft = no
> >
> > ; GENERALIZED BORN ELECTROSTATICS
> > ; Algorithm for calculating Born radii
> > gb_algorithm = Still
> > ; Frequency of calculating the Born radii inside rlist
> > nstgbradii = 1
> > ; Cutoff for Born radii calculation; the contribution from atoms
> > ; between rlist and rgbradii is updated every nstlist steps
> > rgbradii = 2
> > ; Salt concentration in M for Generalized Born models
> > gb_saltconc = 0
> >
> > ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> > implicit_solvent = No
> >
> > ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> > ; Temperature coupling
> > Tcoupl = nose-hoover
> > ; Groups to couple separately
> > tc-grps = DOPS DOPA SOL NA+
> > ; Time constant (ps) and reference temperature (K)
> > tau-t = 0.2 0.2 0.2 0.2
> > ref-t = 303.0 303.0 303.0 303.0
> > ; Pressure coupling
> > Pcoupl = Parrinello-Rahman
> > Pcoupltype = semiisotropic
> > ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> > tau_p = 1.0 1.0
> > compressibility = 4.5e-5 4.5e-5
> > ref_p = 1.01325 1.01325
> > ; Random seed for Andersen thermostat
> > andersen_seed = 815131
> >
> > ; OPTIONS FOR QMMM calculations
> > QMMM = no
> > ; Groups treated Quantum Mechanically
> > QMMM-grps =
> > ; QM method
> > QMmethod =
> > ; QMMM scheme
> > QMMMscheme = normal
> > ; QM basisset
> > QMbasis =
> > ; QM charge
> > QMcharge =
> > ; QM multiplicity
> > QMmult =
> > ; Surface Hopping
> > SH =
> > ; CAS space options
> > CASorbitals =
> > CASelectrons =
> > SAon =
> > SAoff =
> > SAsteps =
> > ; Scale factor for MM charges
> > MMChargeScaleFactor = 1
> > ; Optimization of QM subsystem
> > bOPT =
> > bTS =
> >
> > ; SIMULATED ANNEALING
> > ; Type of annealing for each temperature group (no/single/periodic)
> > annealing = no
> > ; Number of time points to use for specifying annealing in each group
> > annealing_npoints =
> > ; List of times at the annealing points for each group
> > annealing_time =
> > ; Temp. at each annealing point, for each group.
> > annealing_temp =
> >
> > ; GENERATE VELOCITIES FOR STARTUP RUN
> > gen_vel = no
> > gen-temp = 300
> > gen-seed = 533671
> >
> > ; OPTIONS FOR BONDS
> > constraints = all-bonds
> > ; Type of constraint algorithm
> > constraint-algorithm = LINCS
> > ; Do not constrain the start configuration
> > unconstrained-start = yes
> > ; Use successive overrelaxation to reduce the number of shake iterations
> > Shake-SOR = no
> > ; Relative tolerance of shake
> > shake-tol = 0.0001
> > ; Highest order in the expansion of the constraint coupling matrix
> > lincs-order = 4
> > ; Number of iterations in the final step of LINCS. 1 is fine for
> > ; normal simulations, but use 2 to conserve energy in NVE runs.
> > ; For energy minimization with constraints it should be 4 to 8.
> > lincs-iter = 1
> > ; Lincs will write a warning to the stderr if in one step a bond
> > ; rotates over more degrees than
> > lincs-warnangle = 90
> > ; 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) and S to energy file
> > nstorireout = 100
> > ; Dihedral angle restraints: No, Simple or Ensemble
> > dihre = No
> > dihre-fc = 1000
> > dihre-tau = 0
> > ; Output frequency for dihedral values to energy file
> > nstdihreout = 100
> >
> > ; Free energy control stuff
> > free-energy = no
> > init-lambda = 0
> > delta-lambda = 0
> > sc-alpha = 0
> > sc-power = 1
> > sc-sigma = 0.3
> >
> > ; Non-equilibrium MD stuff
> > acc-grps =
> > accelerate =
> > freezegrps =
> > freezedim =
> > cos-acceleration = 0
> > deform =
> >
> > ; 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
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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://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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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://xray.bmc.uu.se/~spoel
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