[gmx-users] pme problems in gromacs 3.3
hseara at netscape.net
hseara at netscape.net
Fri Nov 11 20:07:47 CET 2005
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.
;
; 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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