[gmx-users] pme problems in gromacs 3.3

hseara at netscape.net hseara at netscape.net
Fri Nov 11 20:53:43 CET 2005


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?.
 
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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