Write function to read PDB files and include data for Argon simulation
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
This commit is contained in:
Rafael Ravedutti
parent
ca7775a62a
commit
d0ec9520f2
233
data/anneal.mdp
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233
data/anneal.mdp
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;
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; File 'mdout.mdp' was generated
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; By user: bert (1001)
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; On host: bertp3
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; At date: Sat Dec 4 13:41:42 2004
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;
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; VARIOUS PREPROCESSING OPTIONS
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include =
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define =
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; RUN CONTROL PARAMETERS
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integrator = md
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; Start time and timestep in ps
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tinit = 0
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dt = 0.002
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nsteps = 500000
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; For exact run continuation or redoing part of a run
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init_step = 0
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; mode for center of mass motion removal
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comm-mode = Angular
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; number of steps for center of mass motion removal
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nstcomm = 1
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; group(s) for center of mass motion removal
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comm-grps =
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; LANGEVIN DYNAMICS OPTIONS
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; Temperature, friction coefficient (amu/ps) and random seed
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bd-fric = 0
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ld-seed = 1993
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; ENERGY MINIMIZATION OPTIONS
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; Force tolerance and initial step-size
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emtol = 10
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emstep = 0.01
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; Max number of iterations in relax_shells
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niter = 20
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; Step size (1/ps^2) for minimization of flexible constraints
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fcstep = 0
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; Frequency of steepest descents steps when doing CG
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nstcgsteep = 1000
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nbfgscorr = 10
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; OUTPUT CONTROL OPTIONS
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; Output frequency for coords (x), velocities (v) and forces (f)
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nstxout = 5000
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nstvout = 5000
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nstfout = 0
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; Checkpointing helps you continue after crashes
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nstcheckpoint = 1000
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; Output frequency for energies to log file and energy file
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nstlog = 500
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nstenergy = 500
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; Output frequency and precision for xtc file
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nstxtcout = 500
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xtc-precision = 1000
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; This selects the subset of atoms for the xtc file. You can
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; select multiple groups. By default all atoms will be written.
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xtc-grps =
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; Selection of energy groups
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energygrps = System
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; long-range cut-off for switched potentials
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rlistlong = -1
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cutoff-scheme = Verlet
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; NEIGHBORSEARCHING PARAMETERS
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; nblist update frequency
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nstlist = 50
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; ns algorithm (simple or grid)
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ns_type = grid
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; Periodic boundary conditions: xyz (default), no (vacuum)
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; or full (infinite systems only)
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pbc = xyz
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; nblist cut-off
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rlist = 0.85
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; OPTIONS FOR ELECTROSTATICS AND VDW
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; Method for doing electrostatics
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coulombtype = Cut-off
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rcoulomb-switch = 0
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rcoulomb = 0.85
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; Dielectric constant (DC) for cut-off or DC of reaction field
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epsilon-r = 1
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; Method for doing Van der Waals
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vdw-type = Cut-off
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; cut-off lengths
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rvdw-switch = 0
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rvdw = 0.85
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; Apply long range dispersion corrections for Energy and Pressure
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DispCorr = Enerpres
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; Extension of the potential lookup tables beyond the cut-off
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table-extension = 1
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; Spacing for the PME/PPPM FFT grid
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fourierspacing = 0.12
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; FFT grid size, when a value is 0 fourierspacing will be used
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fourier_nx = 0
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fourier_ny = 0
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fourier_nz = 0
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; EWALD/PME/PPPM parameters
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pme_order = 4
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ewald_rtol = 1e-05
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ewald_geometry = 3d
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epsilon_surface = 0
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optimize_fft = no
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; GENERALIZED BORN ELECTROSTATICS
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; Algorithm for calculating Born radii
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gb_algorithm = Still
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; Frequency of calculating the Born radii inside rlist
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nstgbradii = 1
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; Cutoff for Born radii calculation; the contribution from atoms
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; between rlist and rgbradii is updated every nstlist steps
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rgbradii = 2
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; Salt concentration in M for Generalized Born models
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gb_saltconc = 0
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; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
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implicit_solvent = No
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; OPTIONS FOR WEAK COUPLING ALGORITHMS
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; Temperature coupling
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Tcoupl = v-rescale
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; Groups to couple separately
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tc-grps = System
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; Time constant (ps) and reference temperature (K)
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tau_t = 0.1
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ref_t = 100
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; Pressure coupling
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Pcoupl = no
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Pcoupltype = isotropic
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; Time constant (ps), compressibility (1/bar) and reference P (bar)
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tau_p = 0.5
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compressibility = 4.5e-5
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ref_p = 1.0
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; SIMULATED ANNEALING
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; Type of annealing for each temperature group (no/single/periodic)
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annealing = single
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; Number of time points to use for specifying annealing in each group
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annealing_npoints = 2
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; List of times at the annealing points for each group
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annealing_time = 0 1000
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; Temp. at each annealing point, for each group.
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annealing_temp = 100 25
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; GENERATE VELOCITIES FOR STARTUP RUN
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gen_vel = yes
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gen_temp = 100.0
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gen_seed = 173529
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; OPTIONS FOR BONDS
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constraints = all-bonds
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; Type of constraint algorithm
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constraint-algorithm = Lincs
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; Do not constrain the start configuration
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unconstrained-start = no
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; Use successive overrelaxation to reduce the number of shake iterations
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Shake-SOR = no
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; Relative tolerance of shake
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shake-tol = 1e-04
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; Highest order in the expansion of the constraint coupling matrix
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lincs-order = 4
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; Number of iterations in the final step of LINCS. 1 is fine for
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; normal simulations, but use 2 to conserve energy in NVE runs.
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; For energy minimization with constraints it should be 4 to 8.
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lincs-iter = 1
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; Lincs will write a warning to the stderr if in one step a bond
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; rotates over more degrees than
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lincs-warnangle = 30
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; Convert harmonic bonds to morse potentials
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morse = no
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; ENERGY GROUP EXCLUSIONS
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; Pairs of energy groups for which all non-bonded interactions are excluded
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energygrp_excl =
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; NMR refinement stuff
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; Distance restraints type: No, Simple or Ensemble
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disre = No
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; Force weighting of pairs in one distance restraint: Conservative or Equal
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disre-weighting = Conservative
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; Use sqrt of the time averaged times the instantaneous violation
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disre-mixed = no
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disre-fc = 1000
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disre-tau = 0
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; Output frequency for pair distances to energy file
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nstdisreout = 100
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; Orientation restraints: No or Yes
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orire = no
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; Orientation restraints force constant and tau for time averaging
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orire-fc = 0
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orire-tau = 0
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orire-fitgrp =
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; Output frequency for trace(SD) to energy file
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nstorireout = 100
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; Free energy control stuff
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free-energy = no
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init-lambda = 0
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delta-lambda = 0
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sc-alpha = 0
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sc-sigma = 0.3
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; Non-equilibrium MD stuff
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acc-grps =
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accelerate =
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freezegrps =
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freezedim =
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cos-acceleration = 0
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; Electric fields
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; Format is number of terms (int) and for all terms an amplitude (real)
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; and a phase angle (real)
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E-x =
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E-xt =
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E-y =
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E-yt =
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E-z =
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E-zt =
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; User defined thingies
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user1-grps =
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user2-grps =
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userint1 = 0
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userint2 = 0
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userint3 = 0
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userint4 = 0
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userreal1 = 0
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userreal2 = 0
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userreal3 = 0
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userreal4 = 0
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22
data/argon.top
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22
data/argon.top
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[ defaults ]
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; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
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1 1 no 1.0 1.0
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[ atomtypes ]
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AR 39.948 0.0 A 0.00622127 9.69576e-06
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[ moleculetype ]
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; molname nrexcl
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Ar 1
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[ atoms ]
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; id at type res nr residu name at name cg nr charge
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1 AR 1 Ar Ar 1 0
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[ system ]
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; Name
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Argon
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[ molecules ]
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; Compound #mols
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AR 100
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106
data/argon_start.pdb
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106
data/argon_start.pdb
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HEADER Argon
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REMARK THIS IS A SIMULATION BOX
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CRYST1 77.395 77.395 77.395 90.00 90.00 90.00 P 1 1
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MODEL 1
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ATOM 1 Ar Ar 1 51.580 69.230 34.130 1.00 0.00
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ATOM 2 Ar Ar 2 28.910 66.340 7.590 1.00 0.00
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ATOM 3 Ar Ar 3 43.560 29.320 14.140 1.00 0.00
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ATOM 4 Ar Ar 4 9.020 58.720 19.380 1.00 0.00
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ATOM 5 Ar Ar 5 0.740 15.940 73.580 1.00 0.00
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ATOM 6 Ar Ar 6 61.740 19.620 38.910 1.00 0.00
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ATOM 7 Ar Ar 7 4.440 73.250 49.010 1.00 0.00
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ATOM 8 Ar Ar 8 34.310 35.210 17.110 1.00 0.00
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ATOM 9 Ar Ar 9 27.610 62.240 49.370 1.00 0.00
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ATOM 10 Ar Ar 10 52.470 36.570 24.330 1.00 0.00
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ATOM 11 Ar Ar 11 35.610 40.470 4.600 1.00 0.00
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ATOM 12 Ar Ar 12 11.400 68.530 42.650 1.00 0.00
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ATOM 13 Ar Ar 13 13.360 1.500 72.280 1.00 0.00
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ATOM 14 Ar Ar 14 4.230 22.000 53.780 1.00 0.00
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ATOM 15 Ar Ar 15 43.640 36.730 12.010 1.00 0.00
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ATOM 16 Ar Ar 16 57.390 12.970 74.670 1.00 0.00
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ATOM 17 Ar Ar 17 69.190 24.990 30.900 1.00 0.00
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ATOM 18 Ar Ar 18 8.850 24.190 29.720 1.00 0.00
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ATOM 19 Ar Ar 19 38.950 11.010 71.210 1.00 0.00
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ATOM 20 Ar Ar 20 22.040 2.130 40.060 1.00 0.00
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ATOM 21 Ar Ar 21 5.560 68.420 72.650 1.00 0.00
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ATOM 22 Ar Ar 22 38.530 5.580 63.860 1.00 0.00
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ATOM 23 Ar Ar 23 71.740 31.640 51.650 1.00 0.00
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ATOM 24 Ar Ar 24 63.710 0.640 0.450 1.00 0.00
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ATOM 25 Ar Ar 25 74.000 36.690 65.680 1.00 0.00
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ATOM 26 Ar Ar 26 28.380 38.890 26.020 1.00 0.00
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ATOM 27 Ar Ar 27 34.970 2.100 27.840 1.00 0.00
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ATOM 28 Ar Ar 28 66.720 45.290 70.950 1.00 0.00
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ATOM 29 Ar Ar 29 12.190 55.640 4.650 1.00 0.00
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ATOM 30 Ar Ar 30 19.770 21.860 47.230 1.00 0.00
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ATOM 31 Ar Ar 31 54.140 73.290 39.340 1.00 0.00
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ATOM 32 Ar Ar 32 8.120 34.660 17.400 1.00 0.00
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ATOM 33 Ar Ar 33 16.830 34.030 48.550 1.00 0.00
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ATOM 34 Ar Ar 34 13.390 74.450 6.500 1.00 0.00
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ATOM 35 Ar Ar 35 71.740 3.340 39.860 1.00 0.00
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ATOM 36 Ar Ar 36 30.550 22.140 36.270 1.00 0.00
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ATOM 37 Ar Ar 37 6.670 48.980 36.060 1.00 0.00
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ATOM 38 Ar Ar 38 11.450 29.040 13.290 1.00 0.00
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ATOM 39 Ar Ar 39 26.060 45.780 17.210 1.00 0.00
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ATOM 40 Ar Ar 40 4.010 56.140 37.210 1.00 0.00
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ATOM 41 Ar Ar 41 12.270 39.860 60.810 1.00 0.00
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ATOM 42 Ar Ar 42 26.440 22.380 59.040 1.00 0.00
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ATOM 43 Ar Ar 43 14.010 6.890 63.170 1.00 0.00
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ATOM 44 Ar Ar 44 37.280 58.490 75.890 1.00 0.00
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ATOM 45 Ar Ar 45 34.760 26.610 28.150 1.00 0.00
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ATOM 46 Ar Ar 46 55.310 43.910 71.610 1.00 0.00
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ATOM 47 Ar Ar 47 68.870 73.950 45.180 1.00 0.00
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ATOM 48 Ar Ar 48 50.410 72.800 49.350 1.00 0.00
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ATOM 49 Ar Ar 49 36.760 74.690 32.730 1.00 0.00
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ATOM 50 Ar Ar 50 7.530 68.680 60.120 1.00 0.00
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ATOM 51 Ar Ar 51 23.460 51.370 8.960 1.00 0.00
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ATOM 52 Ar Ar 52 74.590 77.010 7.000 1.00 0.00
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ATOM 53 Ar Ar 53 33.810 36.450 59.930 1.00 0.00
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ATOM 54 Ar Ar 54 62.030 46.010 76.630 1.00 0.00
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ATOM 55 Ar Ar 55 21.890 40.850 12.510 1.00 0.00
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ATOM 56 Ar Ar 56 2.920 71.320 6.370 1.00 0.00
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ATOM 57 Ar Ar 57 8.370 19.070 61.530 1.00 0.00
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ATOM 58 Ar Ar 58 59.620 43.250 34.230 1.00 0.00
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ATOM 59 Ar Ar 59 17.070 9.730 21.600 1.00 0.00
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ATOM 60 Ar Ar 60 68.830 68.080 68.860 1.00 0.00
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ATOM 61 Ar Ar 61 68.990 24.410 0.830 1.00 0.00
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ATOM 62 Ar Ar 62 70.270 66.680 10.930 1.00 0.00
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ATOM 63 Ar Ar 63 60.330 45.690 56.810 1.00 0.00
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ATOM 64 Ar Ar 64 21.780 29.460 18.470 1.00 0.00
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ATOM 65 Ar Ar 65 12.980 48.980 14.410 1.00 0.00
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ATOM 66 Ar Ar 66 27.840 23.230 71.190 1.00 0.00
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ATOM 67 Ar Ar 67 68.140 47.210 22.730 1.00 0.00
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ATOM 68 Ar Ar 68 64.570 54.650 65.550 1.00 0.00
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ATOM 69 Ar Ar 69 70.630 9.780 7.080 1.00 0.00
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ATOM 70 Ar Ar 70 39.870 31.850 4.520 1.00 0.00
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ATOM 71 Ar Ar 71 50.520 19.420 48.020 1.00 0.00
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ATOM 72 Ar Ar 72 52.720 13.230 10.310 1.00 0.00
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ATOM 73 Ar Ar 73 28.900 52.160 60.610 1.00 0.00
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ATOM 74 Ar Ar 74 62.260 40.750 50.970 1.00 0.00
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ATOM 75 Ar Ar 75 55.260 27.540 37.380 1.00 0.00
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ATOM 76 Ar Ar 76 34.160 12.970 17.010 1.00 0.00
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ATOM 77 Ar Ar 77 66.580 17.030 67.060 1.00 0.00
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ATOM 78 Ar Ar 78 70.400 65.440 47.830 1.00 0.00
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ATOM 79 Ar Ar 79 4.550 11.260 19.690 1.00 0.00
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ATOM 80 Ar Ar 80 22.240 6.830 62.670 1.00 0.00
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ATOM 81 Ar Ar 81 58.640 68.400 52.730 1.00 0.00
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ATOM 82 Ar Ar 82 59.810 17.790 5.990 1.00 0.00
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ATOM 83 Ar Ar 83 52.710 76.640 15.370 1.00 0.00
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||||||
|
ATOM 84 Ar Ar 84 61.630 47.230 47.590 1.00 0.00
|
||||||
|
ATOM 85 Ar Ar 85 63.540 70.060 60.590 1.00 0.00
|
||||||
|
ATOM 86 Ar Ar 86 49.310 13.590 71.230 1.00 0.00
|
||||||
|
ATOM 87 Ar Ar 87 14.260 7.730 1.220 1.00 0.00
|
||||||
|
ATOM 88 Ar Ar 88 18.890 50.850 24.650 1.00 0.00
|
||||||
|
ATOM 89 Ar Ar 89 54.320 3.490 35.690 1.00 0.00
|
||||||
|
ATOM 90 Ar Ar 90 57.670 10.710 15.900 1.00 0.00
|
||||||
|
ATOM 91 Ar Ar 91 46.430 0.770 25.020 1.00 0.00
|
||||||
|
ATOM 92 Ar Ar 92 29.450 33.680 34.800 1.00 0.00
|
||||||
|
ATOM 93 Ar Ar 93 58.210 28.400 22.850 1.00 0.00
|
||||||
|
ATOM 94 Ar Ar 94 74.180 19.030 29.610 1.00 0.00
|
||||||
|
ATOM 95 Ar Ar 95 4.810 51.550 14.210 1.00 0.00
|
||||||
|
ATOM 96 Ar Ar 96 20.100 73.430 43.680 1.00 0.00
|
||||||
|
ATOM 97 Ar Ar 97 12.780 4.900 56.140 1.00 0.00
|
||||||
|
ATOM 98 Ar Ar 98 40.120 16.300 64.540 1.00 0.00
|
||||||
|
ATOM 99 Ar Ar 99 55.150 47.800 42.280 1.00 0.00
|
||||||
|
ATOM 100 Ar Ar 100 54.680 31.280 56.510 1.00 0.00
|
||||||
|
TER
|
||||||
|
ENDMDL
|
||||||
233
data/heatup.mdp
Normal file
233
data/heatup.mdp
Normal file
@ -0,0 +1,233 @@
|
|||||||
|
;
|
||||||
|
; File 'mdout.mdp' was generated
|
||||||
|
; By user: bert (1001)
|
||||||
|
; On host: bertp3
|
||||||
|
; At date: Sat Dec 4 13:41:42 2004
|
||||||
|
;
|
||||||
|
|
||||||
|
; VARIOUS PREPROCESSING OPTIONS
|
||||||
|
include =
|
||||||
|
define =
|
||||||
|
|
||||||
|
; RUN CONTROL PARAMETERS
|
||||||
|
integrator = md
|
||||||
|
; Start time and timestep in ps
|
||||||
|
tinit = 0
|
||||||
|
dt = 0.002
|
||||||
|
nsteps = 2500000
|
||||||
|
; For exact run continuation or redoing part of a run
|
||||||
|
init_step = 0
|
||||||
|
; mode for center of mass motion removal
|
||||||
|
comm-mode = Angular
|
||||||
|
; 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-fric = 0
|
||||||
|
ld-seed = 1993
|
||||||
|
|
||||||
|
; ENERGY MINIMIZATION OPTIONS
|
||||||
|
; Force tolerance and initial step-size
|
||||||
|
emtol = 10
|
||||||
|
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
|
||||||
|
nbfgscorr = 10
|
||||||
|
|
||||||
|
; OUTPUT CONTROL OPTIONS
|
||||||
|
; Output frequency for coords (x), velocities (v) and forces (f)
|
||||||
|
nstxout = 5000
|
||||||
|
nstvout = 5000
|
||||||
|
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 = 500
|
||||||
|
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 = System
|
||||||
|
|
||||||
|
; long-range cut-off for switched potentials
|
||||||
|
rlistlong = -1
|
||||||
|
cutoff-scheme = Verlet
|
||||||
|
|
||||||
|
; NEIGHBORSEARCHING PARAMETERS
|
||||||
|
; nblist update frequency
|
||||||
|
nstlist = 50
|
||||||
|
; 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 = 0.85
|
||||||
|
|
||||||
|
|
||||||
|
; OPTIONS FOR ELECTROSTATICS AND VDW
|
||||||
|
; Method for doing electrostatics
|
||||||
|
coulombtype = Cut-off
|
||||||
|
rcoulomb-switch = 0
|
||||||
|
rcoulomb = 0.85
|
||||||
|
; 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
|
||||||
|
rvdw = 0.85
|
||||||
|
; Apply long range dispersion corrections for Energy and Pressure
|
||||||
|
DispCorr = Enerpres
|
||||||
|
; Extension of the potential lookup tables beyond the cut-off
|
||||||
|
table-extension = 1
|
||||||
|
; 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
|
||||||
|
|
||||||
|
; 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 = v-rescale
|
||||||
|
; Groups to couple separately
|
||||||
|
tc-grps = System
|
||||||
|
; Time constant (ps) and reference temperature (K)
|
||||||
|
tau_t = 0.1
|
||||||
|
ref_t = 50
|
||||||
|
; Pressure coupling
|
||||||
|
Pcoupl = no
|
||||||
|
Pcoupltype = isotropic
|
||||||
|
; Time constant (ps), compressibility (1/bar) and reference P (bar)
|
||||||
|
tau_p = 0.5
|
||||||
|
compressibility = 4.5e-5
|
||||||
|
ref_p = 1.0
|
||||||
|
|
||||||
|
; SIMULATED ANNEALING
|
||||||
|
; Type of annealing for each temperature group (no/single/periodic)
|
||||||
|
annealing = single
|
||||||
|
; Number of time points to use for specifying annealing in each group
|
||||||
|
annealing_npoints = 2
|
||||||
|
; List of times at the annealing points for each group
|
||||||
|
annealing_time = 0 5000
|
||||||
|
; Temp. at each annealing point, for each group.
|
||||||
|
annealing_temp = 50 125
|
||||||
|
|
||||||
|
; GENERATE VELOCITIES FOR STARTUP RUN
|
||||||
|
gen_vel = no
|
||||||
|
gen_temp = 0.0
|
||||||
|
gen_seed = 173529
|
||||||
|
|
||||||
|
; OPTIONS FOR BONDS
|
||||||
|
constraints = all-bonds
|
||||||
|
; Type of constraint algorithm
|
||||||
|
constraint-algorithm = Lincs
|
||||||
|
; 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
|
||||||
|
; 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 = 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
|
||||||
233
data/md.mdp
Normal file
233
data/md.mdp
Normal file
@ -0,0 +1,233 @@
|
|||||||
|
;
|
||||||
|
; File 'mdout.mdp' was generated
|
||||||
|
; By user: bert (1001)
|
||||||
|
; On host: bertp3
|
||||||
|
; At date: Sat Dec 4 13:41:42 2004
|
||||||
|
;
|
||||||
|
|
||||||
|
; VARIOUS PREPROCESSING OPTIONS
|
||||||
|
include =
|
||||||
|
define =
|
||||||
|
|
||||||
|
; RUN CONTROL PARAMETERS
|
||||||
|
integrator = md
|
||||||
|
; Start time and timestep in ps
|
||||||
|
tinit = 0
|
||||||
|
dt = 0.002
|
||||||
|
nsteps = 500000
|
||||||
|
; 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
|
||||||
|
; Temperature, friction coefficient (amu/ps) and random seed
|
||||||
|
bd-fric = 0
|
||||||
|
ld-seed = 1993
|
||||||
|
|
||||||
|
; ENERGY MINIMIZATION OPTIONS
|
||||||
|
; Force tolerance and initial step-size
|
||||||
|
emtol = 10
|
||||||
|
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
|
||||||
|
nbfgscorr = 10
|
||||||
|
|
||||||
|
; OUTPUT CONTROL OPTIONS
|
||||||
|
; Output frequency for coords (x), velocities (v) and forces (f)
|
||||||
|
nstxout = 1000
|
||||||
|
nstvout = 1000
|
||||||
|
nstfout = 0
|
||||||
|
; Checkpointing helps you continue after crashes
|
||||||
|
nstcheckpoint = 1000
|
||||||
|
; Output frequency for energies to log file and energy file
|
||||||
|
nstlog = 100
|
||||||
|
nstenergy = 100
|
||||||
|
; Output frequency and precision for xtc file
|
||||||
|
nstxtcout = 500
|
||||||
|
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 = System
|
||||||
|
|
||||||
|
; long-range cut-off for switched potentials
|
||||||
|
rlistlong = -1
|
||||||
|
cutoff-scheme = Verlet
|
||||||
|
|
||||||
|
; NEIGHBORSEARCHING PARAMETERS
|
||||||
|
; nblist update frequency
|
||||||
|
nstlist = 50
|
||||||
|
; 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 = 0.85
|
||||||
|
|
||||||
|
|
||||||
|
; OPTIONS FOR ELECTROSTATICS AND VDW
|
||||||
|
; Method for doing electrostatics
|
||||||
|
coulombtype = Cut-off
|
||||||
|
rcoulomb-switch = 0
|
||||||
|
rcoulomb = 0.85
|
||||||
|
; 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
|
||||||
|
rvdw = 0.85
|
||||||
|
; Apply long range dispersion corrections for Energy and Pressure
|
||||||
|
DispCorr = Enerpres
|
||||||
|
; Extension of the potential lookup tables beyond the cut-off
|
||||||
|
table-extension = 1
|
||||||
|
; 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
|
||||||
|
|
||||||
|
; 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 = v-rescale
|
||||||
|
; Groups to couple separately
|
||||||
|
tc-grps = System
|
||||||
|
; Time constant (ps) and reference temperature (K)
|
||||||
|
tau_t = 0.1
|
||||||
|
ref_t = 100
|
||||||
|
; Pressure coupling
|
||||||
|
Pcoupl = no
|
||||||
|
Pcoupltype = isotropic
|
||||||
|
; Time constant (ps), compressibility (1/bar) and reference P (bar)
|
||||||
|
tau_p = 0.5
|
||||||
|
compressibility = 4.5e-5
|
||||||
|
ref_p = 1.0
|
||||||
|
|
||||||
|
; SIMULATED ANNEALING
|
||||||
|
; Type of annealing for each temperature group (no/single/periodic)
|
||||||
|
annealing =
|
||||||
|
; 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 = yes
|
||||||
|
gen_temp = 100.0
|
||||||
|
gen_seed = 173529
|
||||||
|
|
||||||
|
; OPTIONS FOR BONDS
|
||||||
|
constraints = all-bonds
|
||||||
|
; Type of constraint algorithm
|
||||||
|
constraint-algorithm = Lincs
|
||||||
|
; 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
|
||||||
|
; 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 = 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
|
||||||
106
gromacs/atom.c
106
gromacs/atom.c
@ -168,8 +168,109 @@ void createAtom(Atom *atom, Parameter *param)
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
int readAtom(Atom* atom, Parameter* param)
|
int type_str2int(const char *type) {
|
||||||
{
|
if(strncmp(type, "Ar", 2) == 0) { return 0; } // Argon
|
||||||
|
fprintf(stderr, "Invalid atom type: %s\n", type);
|
||||||
|
exit(-1);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
int readAtom(Atom* atom, Parameter* param) {
|
||||||
|
int len = strlen(param->input_file);
|
||||||
|
if(strncmp(¶m->input_file[len - 4], ".pdb", 4) == 0) { return readAtom_pdb(atom, param); }
|
||||||
|
if(strncmp(¶m->input_file[len - 4], ".dmp", 4) == 0) { return readAtom_dmp(atom, param); }
|
||||||
|
fprintf(stderr, "Invalid input file extension: %s\nValid choices are: pdb, dmp\n", param->input_file);
|
||||||
|
exit(-1);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
int readAtom_pdb(Atom* atom, Parameter* param) {
|
||||||
|
FILE *fp = fopen(param->input_file, "r");
|
||||||
|
char line[MAXLINE];
|
||||||
|
int read_atoms = 0;
|
||||||
|
|
||||||
|
if(!fp) {
|
||||||
|
fprintf(stderr, "Could not open input file: %s\n", param->input_file);
|
||||||
|
exit(-1);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
while(!feof(fp)) {
|
||||||
|
fgets(line, MAXLINE, fp);
|
||||||
|
char *item = strtok(line, " ");
|
||||||
|
if(strncmp(item, "CRYST1", 6) == 0) {
|
||||||
|
param->xlo = 0.0;
|
||||||
|
param->xhi = atof(strtok(NULL, " "));
|
||||||
|
param->ylo = 0.0;
|
||||||
|
param->yhi = atof(strtok(NULL, " "));
|
||||||
|
param->zlo = 0.0;
|
||||||
|
param->zhi = atof(strtok(NULL, " "));
|
||||||
|
param->xprd = param->xhi - param->xlo;
|
||||||
|
param->yprd = param->yhi - param->ylo;
|
||||||
|
param->zprd = param->zhi - param->zlo;
|
||||||
|
// alpha, beta, gamma, sGroup, z
|
||||||
|
} else if(strncmp(item, "ATOM", 4) == 0) {
|
||||||
|
char *label;
|
||||||
|
int atom_id, comp_id;
|
||||||
|
MD_FLOAT occupancy, charge;
|
||||||
|
atom_id = atoi(strtok(NULL, " ")) - 1;
|
||||||
|
|
||||||
|
while(atom_id + 1 >= atom->Nmax) {
|
||||||
|
growAtom(atom);
|
||||||
|
}
|
||||||
|
|
||||||
|
atom->type[atom_id] = type_str2int(strtok(NULL, " "));
|
||||||
|
label = strtok(NULL, " ");
|
||||||
|
comp_id = atoi(strtok(NULL, " "));
|
||||||
|
atom_x(atom_id) = atof(strtok(NULL, " "));
|
||||||
|
atom_y(atom_id) = atof(strtok(NULL, " "));
|
||||||
|
atom_z(atom_id) = atof(strtok(NULL, " "));
|
||||||
|
atom->vx[atom_id] = 0.0;
|
||||||
|
atom->vy[atom_id] = 0.0;
|
||||||
|
atom->vz[atom_id] = 0.0;
|
||||||
|
occupancy = atof(strtok(NULL, " "));
|
||||||
|
charge = atof(strtok(NULL, " "));
|
||||||
|
atom->ntypes = MAX(atom->type[atom_id] + 1, atom->ntypes);
|
||||||
|
atom->Natoms++;
|
||||||
|
atom->Nlocal++;
|
||||||
|
read_atoms++;
|
||||||
|
} else if(strncmp(item, "HEADER", 6) == 0 ||
|
||||||
|
strncmp(item, "REMARK", 6) == 0 ||
|
||||||
|
strncmp(item, "MODEL", 5) == 0 ||
|
||||||
|
strncmp(item, "TER", 3) == 0 ||
|
||||||
|
strncmp(item, "ENDMDL", 6) == 0) {
|
||||||
|
// Do nothing
|
||||||
|
} else {
|
||||||
|
fprintf(stderr, "Invalid item: %s\n", item);
|
||||||
|
exit(-1);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if(!read_atoms) {
|
||||||
|
fprintf(stderr, "Input error: No atoms read!\n");
|
||||||
|
exit(-1);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
atom->epsilon = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
|
||||||
|
atom->sigma6 = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
|
||||||
|
atom->cutforcesq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
|
||||||
|
atom->cutneighsq = allocate(ALIGNMENT, atom->ntypes * atom->ntypes * sizeof(MD_FLOAT));
|
||||||
|
for(int i = 0; i < atom->ntypes * atom->ntypes; i++) {
|
||||||
|
atom->epsilon[i] = param->epsilon;
|
||||||
|
atom->sigma6[i] = param->sigma6;
|
||||||
|
atom->cutneighsq[i] = param->cutneigh * param->cutneigh;
|
||||||
|
atom->cutforcesq[i] = param->cutforce * param->cutforce;
|
||||||
|
}
|
||||||
|
|
||||||
|
fprintf(stdout, "Read %d atoms from %s\n", read_atoms, param->input_file);
|
||||||
|
fclose(fp);
|
||||||
|
return read_atoms;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
int readAtom_dmp(Atom* atom, Parameter* param) {
|
||||||
FILE *fp = fopen(param->input_file, "r");
|
FILE *fp = fopen(param->input_file, "r");
|
||||||
char line[MAXLINE];
|
char line[MAXLINE];
|
||||||
int natoms = 0;
|
int natoms = 0;
|
||||||
@ -258,6 +359,7 @@ int readAtom(Atom* atom, Parameter* param)
|
|||||||
}
|
}
|
||||||
|
|
||||||
fprintf(stdout, "Read %d atoms from %s\n", natoms, param->input_file);
|
fprintf(stdout, "Read %d atoms from %s\n", natoms, param->input_file);
|
||||||
|
fclose(fp);
|
||||||
return natoms;
|
return natoms;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -59,6 +59,8 @@ typedef struct {
|
|||||||
extern void initAtom(Atom*);
|
extern void initAtom(Atom*);
|
||||||
extern void createAtom(Atom*, Parameter*);
|
extern void createAtom(Atom*, Parameter*);
|
||||||
extern int readAtom(Atom*, Parameter*);
|
extern int readAtom(Atom*, Parameter*);
|
||||||
|
extern int readAtom_pdb(Atom*, Parameter*);
|
||||||
|
extern int readAtom_dmp(Atom*, Parameter*);
|
||||||
extern void growAtom(Atom*);
|
extern void growAtom(Atom*);
|
||||||
extern void growClusters(Atom*);
|
extern void growClusters(Atom*);
|
||||||
|
|
||||||
|
|||||||
Loading…
Reference in New Issue
Block a user