Difference between revisions of "Dihedral debugging"
Devicerandom (Talk | contribs) (Created page with "Crude 50 ns simulation of Gly(3) in vacuum. mdp file: -without restraint top file: -with restraint centered on -90, dphi=75") |
Devicerandom (Talk | contribs) |
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+ | <pre> | ||
+ | ; | ||
+ | ; File 'gly3_fullmd__1287526816.mdp' was generated | ||
+ | ; By user: ms872 (1005) | ||
+ | ; On host: nursie | ||
+ | ; At date: Tue Oct 19 23:20:28 2010 | ||
+ | ; | ||
+ | ; VARIOUS PREPROCESSING OPTIONS | ||
+ | ; Preprocessor information: use cpp syntax. | ||
+ | ; e.g.: -I/home/joe/doe -I/home/mary/hoe | ||
+ | include = -I../top | ||
+ | ; e.g.: -DI_Want_Cookies -DMe_Too | ||
+ | define = | ||
− | - | + | ; RUN CONTROL PARAMETERS |
+ | integrator = sd | ||
+ | ; Start time and timestep in ps | ||
+ | tinit = 0 | ||
+ | dt = 0.002 | ||
+ | nsteps = 25000000 | ||
+ | ; For exact run continuation or redoing part of a run | ||
+ | ; Part index is updated automatically on checkpointing (keeps files separate) | ||
+ | simulation_part = 1 | ||
+ | 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 = 10 | ||
+ | emstep = 0.01 | ||
+ | ; Max number of iterations in relax_shells | ||
+ | niter = 20 | ||
+ | ; Step size (ps^2) for minimization of flexible constraints | ||
+ | fcstep = 0 | ||
+ | ; Frequency of steepest descents steps when doing CG | ||
+ | nstcgsteep = 1000 | ||
+ | nbfgscorr = 10 | ||
− | -with restraint | + | ; TEST PARTICLE INSERTION OPTIONS |
+ | rtpi = 0.05 | ||
+ | |||
+ | ; OUTPUT CONTROL OPTIONS | ||
+ | ; Output frequency for coords (x), velocities (v) and forces (f) | ||
+ | nstxout = 1000 | ||
+ | nstvout = 1000 | ||
+ | nstfout = 0 | ||
+ | ; Output frequency for energies to log file and energy file | ||
+ | nstlog = 1000 | ||
+ | nstenergy = 1000 | ||
+ | ; Output frequency and precision for xtc file | ||
+ | nstxtcout = 1000 | ||
+ | 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 = protein | ||
+ | ; Selection of energy groups | ||
+ | energygrps = | ||
+ | |||
+ | ; NEIGHBORSEARCHING PARAMETERS | ||
+ | ; nblist update frequency | ||
+ | nstlist = 10 | ||
+ | ; ns algorithm (simple or grid) | ||
+ | ns_type = grid | ||
+ | ; Periodic boundary conditions: xyz, no, xy | ||
+ | pbc = xyz | ||
+ | periodic_molecules = no | ||
+ | ; nblist cut-off | ||
+ | rlist = 0.8 | ||
+ | |||
+ | ; OPTIONS FOR ELECTROSTATICS AND VDW | ||
+ | ; Method for doing electrostatics | ||
+ | coulombtype = cut-off | ||
+ | rcoulomb-switch = 0 | ||
+ | rcoulomb = 1.4 | ||
+ | ; Relative dielectric constant for the medium and the reaction field | ||
+ | epsilon_r = 1 | ||
+ | epsilon_rf = 1 | ||
+ | ; Method for doing Van der Waals | ||
+ | vdwtype = cut-off | ||
+ | ; cut-off lengths | ||
+ | rvdw-switch = 0 | ||
+ | rvdw = 1.4 | ||
+ | ; Apply long range dispersion corrections for Energy and Pressure | ||
+ | DispCorr = No | ||
+ | ; 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 = 4 | ||
+ | ewald_rtol = 1e-05 | ||
+ | ewald_geometry = 3d | ||
+ | epsilon_surface = 0 | ||
+ | optimize_fft = no | ||
+ | |||
+ | ; IMPLICIT SOLVENT ALGORITHM | ||
+ | implicit_solvent = 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 | ||
+ | ; Dielectric coefficient of the implicit solvent | ||
+ | gb_epsilon_solvent = 80 | ||
+ | ; Salt concentration in M for Generalized Born models | ||
+ | gb_saltconc = 0 | ||
+ | ; Scaling factors used in the OBC GB model. Default values are OBC(II) | ||
+ | gb_obc_alpha = 1 | ||
+ | gb_obc_beta = 0.8 | ||
+ | gb_obc_gamma = 4.85 | ||
+ | ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA | ||
+ | ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. | ||
+ | sa_surface_tension = 2.092 | ||
+ | |||
+ | ; OPTIONS FOR WEAK COUPLING ALGORITHMS | ||
+ | ; Temperature coupling | ||
+ | tcoupl = v-rescale | ||
+ | ; Groups to couple separately | ||
+ | tc-grps = protein | ||
+ | ; Time constant (ps) and reference temperature (K) | ||
+ | tau_t = 2 | ||
+ | ref_t = 300 | ||
+ | ; Pressure coupling | ||
+ | Pcoupl = no | ||
+ | Pcoupltype = Isotropic | ||
+ | ; Time constant (ps), compressibility (1/bar) and reference P (bar) | ||
+ | tau-p = 1 | ||
+ | compressibility = | ||
+ | ref-p = | ||
+ | ; Scaling of reference coordinates, No, All or COM | ||
+ | refcoord_scaling = No | ||
+ | ; 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 = | ||
+ | ; 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 = 300 | ||
+ | gen_seed = 173528 | ||
+ | |||
+ | ; OPTIONS FOR BONDS | ||
+ | constraints = all-bonds | ||
+ | ; Type of constraint algorithm | ||
+ | constraint-algorithm = Lincs | ||
+ | ; Do not constrain the start configuration | ||
+ | continuation = no | ||
+ | ; 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 = 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 = | ||
+ | |||
+ | ; WALLS | ||
+ | ; Number of walls, type, atom types, densities and box-z scale factor for Ewald | ||
+ | nwall = 0 | ||
+ | wall_type = 9-3 | ||
+ | wall_r_linpot = -1 | ||
+ | wall_atomtype = | ||
+ | wall_density = | ||
+ | wall_ewald_zfac = 3 | ||
+ | |||
+ | ; COM PULLING | ||
+ | ; Pull type: no, umbrella, constraint or constant_force | ||
+ | pull = no | ||
+ | |||
+ | ; 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 or Yes | ||
+ | dihre = yes | ||
+ | dihre_fc = 10 | ||
+ | |||
+ | ; Free energy control stuff | ||
+ | free-energy = no | ||
+ | init-lambda = 0 | ||
+ | delta-lambda = 0 | ||
+ | sc-alpha = 0 | ||
+ | sc-power = 0 | ||
+ | sc-sigma = 0.3 | ||
+ | couple-moltype = | ||
+ | couple-lambda0 = vdw-q | ||
+ | couple-lambda1 = vdw-q | ||
+ | couple-intramol = no | ||
+ | |||
+ | ; 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 | ||
+ | </pre> | ||
+ | |||
+ | top file (here with restraint - without is identical except it lacks the [ dihedral restraint ] section): | ||
+ | <pre> | ||
+ | ; | ||
+ | ; File 'gly3.top' was generated | ||
+ | ; By user: ms872 (1005) | ||
+ | ; On host: nursie | ||
+ | ; At date: Tue Oct 19 23:07:48 2010 | ||
+ | ; | ||
+ | ; This is your topology file | ||
+ | ; "Fresh Air, Green Hair" (Frank Black) | ||
+ | ; | ||
+ | ; Include forcefield parameters | ||
+ | #include "ffoplsaa.itp" | ||
+ | |||
+ | [ moleculetype ] | ||
+ | ; Name nrexcl | ||
+ | Protein 3 | ||
+ | |||
+ | [ atoms ] | ||
+ | ; nr type resnr residue atom cgnr charge mass typeB chargeB massB | ||
+ | 1 opls_900 1 GLY N 1 -0.9 14.0067 ; qtot -0.9 | ||
+ | 2 opls_909 1 GLY H1 1 0.36 1.008 ; qtot -0.54 | ||
+ | 3 opls_909 1 GLY H2 1 0.36 1.008 ; qtot -0.18 | ||
+ | 4 opls_906B 1 GLY CA 1 0.06 12.011 ; qtot -0.12 | ||
+ | 5 opls_140 1 GLY HA1 1 0.06 1.008 ; qtot -0.06 | ||
+ | 6 opls_140 1 GLY HA2 1 0.06 1.008 ; qtot 0 | ||
+ | 7 opls_235 1 GLY C 2 0.5 12.011 ; qtot 0.5 | ||
+ | 8 opls_236 1 GLY O 2 -0.5 15.9994 ; qtot 0 | ||
+ | 9 opls_238 2 GLY N 3 -0.5 14.0067 ; qtot -0.5 | ||
+ | 10 opls_241 2 GLY H 3 0.3 1.008 ; qtot -0.2 | ||
+ | 11 opls_223B 2 GLY CA 3 0.08 12.011 ; qtot -0.12 | ||
+ | 12 opls_140 2 GLY HA1 3 0.06 1.008 ; qtot -0.06 | ||
+ | 13 opls_140 2 GLY HA2 3 0.06 1.008 ; qtot 0 | ||
+ | 14 opls_235 2 GLY C 4 0.5 12.011 ; qtot 0.5 | ||
+ | 15 opls_236 2 GLY O 4 -0.5 15.9994 ; qtot 0 | ||
+ | 16 opls_238 3 GLY N 5 -0.5 14.0067 ; qtot -0.5 | ||
+ | 17 opls_241 3 GLY H 5 0.3 1.008 ; qtot -0.2 | ||
+ | 18 opls_223B 3 GLY CA 5 0.08 12.011 ; qtot -0.12 | ||
+ | 19 opls_140 3 GLY HA1 5 0.06 1.008 ; qtot -0.06 | ||
+ | 20 opls_140 3 GLY HA2 5 0.06 1.008 ; qtot 0 | ||
+ | 21 opls_267 3 GLY C 6 0.52 12.011 ; qtot 0.52 | ||
+ | 22 opls_269 3 GLY OT 6 -0.44 15.9994 ; qtot 0.08 | ||
+ | 23 opls_268 3 GLY O 6 -0.53 15.9994 ; qtot -0.45 | ||
+ | 24 opls_270 3 GLY HO 6 0.45 1.008 ; qtot 0 | ||
+ | |||
+ | |||
+ | |||
+ | [ dihedral_restraints ] | ||
+ | ; ai aj ak al type label phi dphi kfac power | ||
+ | ; phi C'(n-1) - N - CA - C' | ||
+ | 7 9 11 14 1 1 -90 75 2 1 | ||
+ | 14 16 18 21 1 1 -90 75 2 1 | ||
+ | |||
+ | |||
+ | [ bonds ] | ||
+ | ; ai aj funct c0 c1 c2 c3 | ||
+ | 1 2 1 | ||
+ | 1 3 1 | ||
+ | 1 4 1 | ||
+ | 4 5 1 | ||
+ | 4 6 1 | ||
+ | 4 7 1 | ||
+ | 7 8 1 | ||
+ | 7 9 1 | ||
+ | 9 10 1 | ||
+ | 9 11 1 | ||
+ | 11 12 1 | ||
+ | 11 13 1 | ||
+ | 11 14 1 | ||
+ | 14 15 1 | ||
+ | 14 16 1 | ||
+ | 16 17 1 | ||
+ | 16 18 1 | ||
+ | 18 19 1 | ||
+ | 18 20 1 | ||
+ | 18 21 1 | ||
+ | 21 22 1 | ||
+ | 21 23 1 | ||
+ | 23 24 1 | ||
+ | |||
+ | [ pairs ] | ||
+ | ; ai aj funct c0 c1 c2 c3 | ||
+ | 1 8 1 | ||
+ | 1 9 1 | ||
+ | 2 5 1 | ||
+ | 2 6 1 | ||
+ | 2 7 1 | ||
+ | 3 5 1 | ||
+ | 3 6 1 | ||
+ | 3 7 1 | ||
+ | 4 10 1 | ||
+ | 4 11 1 | ||
+ | 5 8 1 | ||
+ | 5 9 1 | ||
+ | 6 8 1 | ||
+ | 6 9 1 | ||
+ | 7 12 1 | ||
+ | 7 13 1 | ||
+ | 7 14 1 | ||
+ | 8 10 1 | ||
+ | 8 11 1 | ||
+ | 9 15 1 | ||
+ | 9 16 1 | ||
+ | 10 12 1 | ||
+ | 10 13 1 | ||
+ | 10 14 1 | ||
+ | 11 17 1 | ||
+ | 11 18 1 | ||
+ | 12 15 1 | ||
+ | 12 16 1 | ||
+ | 13 15 1 | ||
+ | 13 16 1 | ||
+ | 14 19 1 | ||
+ | 14 20 1 | ||
+ | 14 21 1 | ||
+ | 15 17 1 | ||
+ | 15 18 1 | ||
+ | 16 22 1 | ||
+ | 16 23 1 | ||
+ | 17 19 1 | ||
+ | 17 20 1 | ||
+ | 17 21 1 | ||
+ | 18 24 1 | ||
+ | 19 22 1 | ||
+ | 19 23 1 | ||
+ | 20 22 1 | ||
+ | 20 23 1 | ||
+ | 22 24 1 | ||
+ | |||
+ | [ angles ] | ||
+ | ; ai aj ak funct c0 c1 c2 c3 | ||
+ | 2 1 3 1 | ||
+ | 2 1 4 1 | ||
+ | 3 1 4 1 | ||
+ | 1 4 5 1 | ||
+ | 1 4 6 1 | ||
+ | 1 4 7 1 | ||
+ | 5 4 6 1 | ||
+ | 5 4 7 1 | ||
+ | 6 4 7 1 | ||
+ | 4 7 8 1 | ||
+ | 4 7 9 1 | ||
+ | 8 7 9 1 | ||
+ | 7 9 10 1 | ||
+ | 7 9 11 1 | ||
+ | 10 9 11 1 | ||
+ | 9 11 12 1 | ||
+ | 9 11 13 1 | ||
+ | 9 11 14 1 | ||
+ | 12 11 13 1 | ||
+ | 12 11 14 1 | ||
+ | 13 11 14 1 | ||
+ | 11 14 15 1 | ||
+ | 11 14 16 1 | ||
+ | 15 14 16 1 | ||
+ | 14 16 17 1 | ||
+ | 14 16 18 1 | ||
+ | 17 16 18 1 | ||
+ | 16 18 19 1 | ||
+ | 16 18 20 1 | ||
+ | 16 18 21 1 | ||
+ | 19 18 20 1 | ||
+ | 19 18 21 1 | ||
+ | 20 18 21 1 | ||
+ | 18 21 22 1 | ||
+ | 18 21 23 1 | ||
+ | 22 21 23 1 | ||
+ | 21 23 24 1 | ||
+ | |||
+ | [ dihedrals ] | ||
+ | ; ai aj ak al funct c0 c1 c2 c3 c4 c5 | ||
+ | 2 1 4 5 3 | ||
+ | 2 1 4 6 3 | ||
+ | 2 1 4 7 3 | ||
+ | 3 1 4 5 3 | ||
+ | 3 1 4 6 3 | ||
+ | 3 1 4 7 3 | ||
+ | 1 4 7 8 3 | ||
+ | 1 4 7 9 3 | ||
+ | 5 4 7 8 3 | ||
+ | 5 4 7 9 3 | ||
+ | 6 4 7 8 3 | ||
+ | 6 4 7 9 3 | ||
+ | 4 7 9 10 3 | ||
+ | 4 7 9 11 3 | ||
+ | 8 7 9 10 3 | ||
+ | 8 7 9 11 3 | ||
+ | 7 9 11 12 3 | ||
+ | 7 9 11 13 3 | ||
+ | 7 9 11 14 3 | ||
+ | 10 9 11 12 3 | ||
+ | 10 9 11 13 3 | ||
+ | 10 9 11 14 3 | ||
+ | 9 11 14 15 3 | ||
+ | 9 11 14 16 3 | ||
+ | 12 11 14 15 3 | ||
+ | 12 11 14 16 3 | ||
+ | 13 11 14 15 3 | ||
+ | 13 11 14 16 3 | ||
+ | 11 14 16 17 3 | ||
+ | 11 14 16 18 3 | ||
+ | 15 14 16 17 3 | ||
+ | 15 14 16 18 3 | ||
+ | 14 16 18 19 3 | ||
+ | 14 16 18 20 3 | ||
+ | 14 16 18 21 3 | ||
+ | 17 16 18 19 3 | ||
+ | 17 16 18 20 3 | ||
+ | 17 16 18 21 3 | ||
+ | 16 18 21 22 3 | ||
+ | 16 18 21 23 3 | ||
+ | 19 18 21 22 3 | ||
+ | 19 18 21 23 3 | ||
+ | 20 18 21 22 3 | ||
+ | 20 18 21 23 3 | ||
+ | 18 21 23 24 3 | ||
+ | 22 21 23 24 3 | ||
+ | |||
+ | [ dihedrals ] | ||
+ | ; ai aj ak al funct c0 c1 c2 c3 | ||
+ | 4 9 7 8 1 improper_O_C_X_Y | ||
+ | 7 11 9 10 1 improper_Z_N_X_Y | ||
+ | 11 16 14 15 1 improper_O_C_X_Y | ||
+ | 14 18 16 17 1 improper_Z_N_X_Y | ||
+ | 18 22 21 23 1 improper_O_C_X_Y | ||
+ | |||
+ | ; Include Position restraint file | ||
+ | #ifdef POSRES | ||
+ | #include "posre.itp" | ||
+ | #endif | ||
+ | |||
+ | ; Include water topology | ||
+ | #include "spc.itp" | ||
+ | |||
+ | #ifdef POSRES_WATER | ||
+ | ; Position restraint for each water oxygen | ||
+ | [ position_restraints ] | ||
+ | ; i funct fcx fcy fcz | ||
+ | 1 1 1000 1000 1000 | ||
+ | #endif | ||
+ | |||
+ | ; Include generic topology for ions | ||
+ | #include "ions.itp" | ||
+ | |||
+ | [ system ] | ||
+ | ; Name | ||
+ | Protein | ||
+ | |||
+ | [ molecules ] | ||
+ | ; Compound #mols | ||
+ | Protein 1 | ||
+ | </pre> |
Revision as of 13:04, 20 October 2010
Crude 50 ns simulation of Gly(3) in vacuum.
mdp file:
; ; File 'gly3_fullmd__1287526816.mdp' was generated ; By user: ms872 (1005) ; On host: nursie ; At date: Tue Oct 19 23:20:28 2010 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = -I../top ; e.g.: -DI_Want_Cookies -DMe_Too define = ; RUN CONTROL PARAMETERS integrator = sd ; Start time and timestep in ps tinit = 0 dt = 0.002 nsteps = 25000000 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 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 = 10 emstep = 0.01 ; Max number of iterations in relax_shells niter = 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr = 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file nstxtcout = 1000 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 = protein ; Selection of energy groups energygrps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist = 0.8 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = cut-off rcoulomb-switch = 0 rcoulomb = 1.4 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Method for doing Van der Waals vdwtype = cut-off ; cut-off lengths rvdw-switch = 0 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; 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 = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = 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 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. sa_surface_tension = 2.092 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling tcoupl = v-rescale ; Groups to couple separately tc-grps = protein ; Time constant (ps) and reference temperature (K) tau_t = 2 ref_t = 300 ; Pressure coupling Pcoupl = no Pcoupltype = Isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1 compressibility = ref-p = ; Scaling of reference coordinates, No, All or COM refcoord_scaling = No ; 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 = ; 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 = 300 gen_seed = 173528 ; OPTIONS FOR BONDS constraints = all-bonds ; Type of constraint algorithm constraint-algorithm = Lincs ; Do not constrain the start configuration continuation = no ; 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 = 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 = ; WALLS ; Number of walls, type, atom types, densities and box-z scale factor for Ewald nwall = 0 wall_type = 9-3 wall_r_linpot = -1 wall_atomtype = wall_density = wall_ewald_zfac = 3 ; COM PULLING ; Pull type: no, umbrella, constraint or constant_force pull = no ; 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 or Yes dihre = yes dihre_fc = 10 ; Free energy control stuff free-energy = no init-lambda = 0 delta-lambda = 0 sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no ; 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
top file (here with restraint - without is identical except it lacks the [ dihedral restraint ] section):
; ; File 'gly3.top' was generated ; By user: ms872 (1005) ; On host: nursie ; At date: Tue Oct 19 23:07:48 2010 ; ; This is your topology file ; "Fresh Air, Green Hair" (Frank Black) ; ; Include forcefield parameters #include "ffoplsaa.itp" [ moleculetype ] ; Name nrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_900 1 GLY N 1 -0.9 14.0067 ; qtot -0.9 2 opls_909 1 GLY H1 1 0.36 1.008 ; qtot -0.54 3 opls_909 1 GLY H2 1 0.36 1.008 ; qtot -0.18 4 opls_906B 1 GLY CA 1 0.06 12.011 ; qtot -0.12 5 opls_140 1 GLY HA1 1 0.06 1.008 ; qtot -0.06 6 opls_140 1 GLY HA2 1 0.06 1.008 ; qtot 0 7 opls_235 1 GLY C 2 0.5 12.011 ; qtot 0.5 8 opls_236 1 GLY O 2 -0.5 15.9994 ; qtot 0 9 opls_238 2 GLY N 3 -0.5 14.0067 ; qtot -0.5 10 opls_241 2 GLY H 3 0.3 1.008 ; qtot -0.2 11 opls_223B 2 GLY CA 3 0.08 12.011 ; qtot -0.12 12 opls_140 2 GLY HA1 3 0.06 1.008 ; qtot -0.06 13 opls_140 2 GLY HA2 3 0.06 1.008 ; qtot 0 14 opls_235 2 GLY C 4 0.5 12.011 ; qtot 0.5 15 opls_236 2 GLY O 4 -0.5 15.9994 ; qtot 0 16 opls_238 3 GLY N 5 -0.5 14.0067 ; qtot -0.5 17 opls_241 3 GLY H 5 0.3 1.008 ; qtot -0.2 18 opls_223B 3 GLY CA 5 0.08 12.011 ; qtot -0.12 19 opls_140 3 GLY HA1 5 0.06 1.008 ; qtot -0.06 20 opls_140 3 GLY HA2 5 0.06 1.008 ; qtot 0 21 opls_267 3 GLY C 6 0.52 12.011 ; qtot 0.52 22 opls_269 3 GLY OT 6 -0.44 15.9994 ; qtot 0.08 23 opls_268 3 GLY O 6 -0.53 15.9994 ; qtot -0.45 24 opls_270 3 GLY HO 6 0.45 1.008 ; qtot 0 [ dihedral_restraints ] ; ai aj ak al type label phi dphi kfac power ; phi C'(n-1) - N - CA - C' 7 9 11 14 1 1 -90 75 2 1 14 16 18 21 1 1 -90 75 2 1 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 1 1 3 1 1 4 1 4 5 1 4 6 1 4 7 1 7 8 1 7 9 1 9 10 1 9 11 1 11 12 1 11 13 1 11 14 1 14 15 1 14 16 1 16 17 1 16 18 1 18 19 1 18 20 1 18 21 1 21 22 1 21 23 1 23 24 1 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 8 1 1 9 1 2 5 1 2 6 1 2 7 1 3 5 1 3 6 1 3 7 1 4 10 1 4 11 1 5 8 1 5 9 1 6 8 1 6 9 1 7 12 1 7 13 1 7 14 1 8 10 1 8 11 1 9 15 1 9 16 1 10 12 1 10 13 1 10 14 1 11 17 1 11 18 1 12 15 1 12 16 1 13 15 1 13 16 1 14 19 1 14 20 1 14 21 1 15 17 1 15 18 1 16 22 1 16 23 1 17 19 1 17 20 1 17 21 1 18 24 1 19 22 1 19 23 1 20 22 1 20 23 1 22 24 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 3 1 2 1 4 1 3 1 4 1 1 4 5 1 1 4 6 1 1 4 7 1 5 4 6 1 5 4 7 1 6 4 7 1 4 7 8 1 4 7 9 1 8 7 9 1 7 9 10 1 7 9 11 1 10 9 11 1 9 11 12 1 9 11 13 1 9 11 14 1 12 11 13 1 12 11 14 1 13 11 14 1 11 14 15 1 11 14 16 1 15 14 16 1 14 16 17 1 14 16 18 1 17 16 18 1 16 18 19 1 16 18 20 1 16 18 21 1 19 18 20 1 19 18 21 1 20 18 21 1 18 21 22 1 18 21 23 1 22 21 23 1 21 23 24 1 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 2 1 4 5 3 2 1 4 6 3 2 1 4 7 3 3 1 4 5 3 3 1 4 6 3 3 1 4 7 3 1 4 7 8 3 1 4 7 9 3 5 4 7 8 3 5 4 7 9 3 6 4 7 8 3 6 4 7 9 3 4 7 9 10 3 4 7 9 11 3 8 7 9 10 3 8 7 9 11 3 7 9 11 12 3 7 9 11 13 3 7 9 11 14 3 10 9 11 12 3 10 9 11 13 3 10 9 11 14 3 9 11 14 15 3 9 11 14 16 3 12 11 14 15 3 12 11 14 16 3 13 11 14 15 3 13 11 14 16 3 11 14 16 17 3 11 14 16 18 3 15 14 16 17 3 15 14 16 18 3 14 16 18 19 3 14 16 18 20 3 14 16 18 21 3 17 16 18 19 3 17 16 18 20 3 17 16 18 21 3 16 18 21 22 3 16 18 21 23 3 19 18 21 22 3 19 18 21 23 3 20 18 21 22 3 20 18 21 23 3 18 21 23 24 3 22 21 23 24 3 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 4 9 7 8 1 improper_O_C_X_Y 7 11 9 10 1 improper_Z_N_X_Y 11 16 14 15 1 improper_O_C_X_Y 14 18 16 17 1 improper_Z_N_X_Y 18 22 21 23 1 improper_O_C_X_Y ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein 1