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.mdp File
From $1
Simulation parameter input file for grompp.
Defines the parameters for running the simulation, including time step, type of simulation, electrostatics, van der Waals, temperature coupling, pressure coupling, etc.
See GROMACS Manual, Section 7.3 and mdp options, Online Manual.
Options
- preprocessing (title, warnings, cpp, include, define)
- run control (integrator, tinit, dt, nsteps, init_step, comm_mode, nstcomm, comm_grps)
- langevin dynamics (bd_fric, ld_seed)
- energy minimization (emtol, emstep, nstcgsteep)
- shell molecular dynamics (emtol,niter,fcstep)
- output control (nstxout, nstvout, nstfout, nstlog, nstenergy, nstxtcout, xtc_precision, xtc_grps, energygrps)
- neighbor searching (nstlist, ns_type, pbc, rlist)
- electrostatics (coulombtype, rcoulomb_switch, rcoulomb, epsilon_r, epsilon_rf)
- VdW (vdwtype, rvdw_switch, rvdw, DispCorr)
- tables (table-extension, energygrp_table)
- Ewald (fourierspacing, fourier_nx, fourier_ny, fourier_nz, pme_order, ewald_rtol, ewald_geometry, epsilon_surface, optimize_fft)
- Temperature coupling (tcoupl, tc_grps, tau_t, ref_t)
- Pressure coupling (pcoupl, pcoupltype, tau_p, compressibility, ref_p)
- simulated annealing (annealing, annealing_npoints, annealing_time, annealing_temp)
- velocity generation (gen_vel, gen_temp, gen_seed)
- bonds (constraints, constraint_algorithm, unconstrained_start, shake_tol, lincs_order, lincs_iter, lincs_warnangle, morse)
- Energy group exclusions (energygrp_excl)
- NMR refinement (disre, disre_weighting, disre_mixed, disre_fc, disre_tau, nstdisreout, orire, orire_fc, orire_tau, orire_fitgrp, nstorireout)
- Free Energy Perturbation (free_energy, init_lambda, delta_lambda, sc_alpha, sc_power, sc_sigma)
- Non-equilibrium MD (acc_grps, accelerate, freezegrps, freezedim, cos_acceleration, deform)
- Electric fields (E_x, E_xt, E_y, E_yt, E_z, E_zt )
- Mixed quantum/classical dynamics (QMMM, QMMM-grps, QMMMscheme, QMmethod, QMbasis, QMcharge, Qmmult, CASorbitals, CASelectrons, SH)
- User defined thingies (user1_grps, user2_grps, userint1, userint2, userint3, userint4, userreal1, userreal2, userreal3, userreal4)
- Index
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