Ubq min.mdp
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; 7.3.2 Preprocessing define = -DFLEXIBLE ; defines to pass to the preprocessor ; 7.3.3 Run Control integrator = steep ; steepest descents energy minimization nsteps = 2000 ; maximum number of steps to integrate ; 7.3.5 Energy Minimization emtol = 1000 ; [kJ/mol/nm] minimization is converged when max force is < emtol emstep = 0.01 ; [nm] initial step-size ; 7.3.8 Output Control nstxout = 100 ; [steps] freq to write coordinates to trajectory nstvout = 100 ; [steps] freq to write velocities to trajectory nstfout = 100 ; [steps] freq to write forces to trajectory nstlog = 1 ; [steps] freq to write energies to log file nstenergy = 1 ; [steps] freq to write energies to energy file energygrps = System ; group(s) to write to energy file ; 7.3.9 Neighbor Searching nstlist = 1 ; [steps] freq to update neighbor list ns_type = grid ; method of updating neighbor list pbc = xyz ; periodic boundary conditions in all directions rlist = 0.8 ; [nm] cut-off distance for the short-range neighbor list ; 7.3.10 Electrostatics coulombtype = PME ; Particle-Mesh Ewald electrostatics rcoulomb = 0.8 ; [nm] distance for Coulomb cut-off ; 7.3.11 VdW vdwtype = cut-off ; twin-range cut-off with rlist where rvdw >= rlist rvdw = 0.8 ; [nm] distance for LJ cut-off DispCorr = Ener ; apply long range dispersion corrections for energy ; 7.3.13 Ewald fourierspacing = 0.12 ; [nm] grid spacing for FFT grid when using PME pme_order = 4 ; interpolation order for PME, 4 = cubic ewald_rtol = 1e-5 ; relative strength of Ewald-shifted potential at rcoulomb
