Dear Gromacs Users:<br>I've been working with small unsaturated hydrocarbons using OPLS-AA with NVT calculations using box dimensions according to : x=y & z=3x centered in 1/2x,1/2y,1/2z in order to obtain surface tension. My system expands at the begging of the mdrun calculation until it occupies the whole box uniformly. <br>
The mdp file i'm using its:<br><br>; VARIOUS PREPROCESSING OPTIONS<br>title = Yo<br>cpp = /usr/bin/cpp<br>include =<br>define =<br><br>; RUN CONTROL PARAMETERS<br>
integrator = md<br>; Start time and timestep in ps<br>tinit = 0<br>dt = 0.003<br>nsteps = 400000<br>; For exact run continuation or redoing part of a run<br>
init_step = 0<br>; mode for center of mass motion removal<br>comm-mode = Linear<br>; number of steps for center of mass motion removal<br>nstcomm = 1<br>; group(s) for center of mass motion removal<br>
comm-grps =<br><br>; LANGEVIN DYNAMICS OPTIONS<br>; Temperature, friction coefficient (amu/ps) and random seed<br>;bd-temp = 300<br>;bd-fric = 0<br>;ld-seed = 1993<br>
<br>; ENERGY MINIMIZATION OPTIONS<br>; Force tolerance and initial step-size<br>emtol = 100<br>emstep = 0.01<br>; Max number of iterations in relax_shells<br>niter = 20<br>
; Step size (1/ps^2) for minimization of flexible constraints<br>fcstep = 0<br>; Frequency of steepest descents steps when doing CG<br>nstcgsteep = 1000<br>nbfgscorr = 10<br>
<br>; OUTPUT CONTROL OPTIONS<br>; Output frequency for coords (x), velocities (v) and forces (f)<br>nstxout = 1000<br>nstvout = 1000<br>nstfout = 1000<br>; Checkpointing helps you continue after crashes<br>
nstcheckpoint = 1000<br>; Output frequency for energies to log file and energy file<br>nstlog = 50<br>nstenergy = 50<br>; Output frequency and precision for xtc file<br>nstxtcout = 50<br>
xtc-precision = 1000<br>; This selects the subset of atoms for the xtc file. You can<br>; select multiple groups. By default all atoms will be written.<br>xtc-grps =<br>; Selection of energy groups<br>
energygrps =<br><br>; NEIGHBORSEARCHING PARAMETERS<br>; nblist update frequency<br>nstlist = 5<br>; ns algorithm (simple or grid)<br>ns_type = grid<br>; Periodic boundary conditions: xyz (default), no (vacuum)<br>
; or full (infinite systems only)<br>pbc = xyz<br>; nblist cut-off<br>rlist = 1.4<br>domain-decomposition = no<br><br>; OPTIONS FOR ELECTROSTATICS AND VDW<br>; Method for doing electrostatics<br>
coulombtype = PME<br>rcoulomb-switch = 0<br>rcoulomb = 1.4<br>; Dielectric constant (DC) for cut-off or DC of reaction field<br>epsilon-r = 1<br>; Method for doing Van der Waals<br>
vdw-type = Cut-off<br>; cut-off lengths<br>rvdw-switch = 0<br>rvdw = 1.4<br>; Apply long range dispersion corrections for Energy and Pressure<br>DispCorr = EnerPres<br>
; Extension of the potential lookup tables beyond the cut-off<br>table-extension = 1<br>; Spacing for the PME/PPPM FFT grid<br>fourierspacing = 0.12<br>; FFT grid size, when a value is 0 fourierspacing will be used<br>
fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>; EWALD/PME/PPPM parameters<br>pme_order = 4<br>ewald_rtol = 1e-05<br>ewald_geometry = 3d<br>
epsilon_surface = 0<br>optimize_fft = no<br><br>; GENERALIZED BORN ELECTROSTATICS<br>; Algorithm for calculating Born radii<br>gb_algorithm = Still<br>; Frequency of calculating the Born radii inside rlist<br>
nstgbradii = 1<br>; Cutoff for Born radii calculation; the contribution from atoms<br>; between rlist and rgbradii is updated every nstlist steps<br>rgbradii = 2<br>; Salt concentration in M for Generalized Born models<br>
gb_saltconc = 0<br>; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)<br>implicit_solvent = No<br><br>; OPTIONS FOR WEAK COUPLING ALGORITHMS<br>; Temperature coupling<br>Tcoupl = berendsen<br>
; Groups to couple separately<br>tc-grps = System<br>; Time constant (ps) and reference temperature (K)<br>tau_t = 0.1<br>ref_t = 330<br>; Pressure coupling<br>Pcoupl = no<br>
Pcoupltype = isotropic<br>; Time constant (ps), compressibility (1/bar) and reference P (bar)<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Random seed for Andersen thermostat<br>
ondersen_seed = 815131<br><br><br><br><br>; SIMULATED ANNEALING<br>; Type of annealing for each temperature group (no/single/periodic)<br>annealing = no<br>; Number of time points to use for specifying annealing in each group<br>
annealing_npoints =<br>; List of times at the annealing points for each group<br>annealing_time =<br>; Temp. at each annealing point, for each group.<br>annealing_temp =<br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>
gen_vel = yes<br>gen_temp = 300<br>gen_seed = 1993<br><br>; OPTIONS FOR BONDS<br>constraints = all-bonds<br>; Type of constraint algorithm<br>constraint-algorithm = Lincs<br>
; Do not constrain the start configuration<br>unconstrained-start = no<br>; Use successive overrelaxation to reduce the number of shake iterations<br>Shake-SOR = no<br>; Relative tolerance of shake<br>
shake-tol = 1e-04<br>; Highest order in the expansion of the constraint coupling matrix<br>lincs-order = -1<br>; Number of iterations in the final step of LINCS. 1 is fine for<br>; normal simulations, but use 2 to conserve energy in NVE runs.<br>
; For energy minimization with constraints it should be 4 to 8.<br>lincs-iter = 1<br>; Lincs will write a warning to the stderr if in one step a bond<br>; rotates over more degrees than<br>lincs-warnangle = 30<br>
; Convert harmonic bonds to morse potentials<br>morse = no<br><br>; ENERGY GROUP EXCLUSIONS<br>; Pairs of energy groups for which all non-bonded interactions are excluded<br>energygrp_excl =<br>
<br>; NMR refinement stuff<br>; Distance restraints type: No, Simple or Ensemble<br>disre = No<br>; Force weighting of pairs in one distance restraint: Conservative or Equal<br>disre-weighting = Conservative<br>
; Use sqrt of the time averaged times the instantaneous violation<br>disre-mixed = no<br>disre-fc = 1000<br>disre-tau = 0<br>; Output frequency for pair distances to energy file<br>
nstdisreout = 100<br>; Orientation restraints: No or Yes<br>orire = no<br>; Orientation restraints force constant and tau for time averaging<br>orire-fc = 0<br>orire-tau = 0<br>
orire-fitgrp =<br>; Output frequency for trace(SD) to energy file<br>nstorireout = 100<br>; Dihedral angle restraints: No, Simple or Ensemble<br>dihre = No<br>dihre-fc = 1000<br>
dihre-tau = 0<br>; Output frequency for dihedral values to energy file<br>nstdihreout = 100<br><br>