# Ubq md.mdp

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; 7.3.3 Run Control integrator = md ; md integrator tinit = 0 ; [ps] starting time for run dt = 0.002 ; [ps] time step for integration nsteps = 2500000 ; maximum number of steps to integrate, 0.002 * 2,500,000 = 5,000 ps comm_mode = Linear ; remove center of mass translation nstcomm = 1 ; [steps] frequency of mass motion removal comm_grps = Protein Non-Protein ; group(s) for center of mass motion removal ; 7.3.8 Output Control nstxout = 2500000 ; [steps] freq to write coordinates to trajectory nstvout = 2500000 ; [steps] freq to write velocities to trajectory nstfout = 2500000 ; [steps] freq to write forces to trajectory nstlog = 100 ; [steps] freq to write energies to log file nstenergy = 500 ; [steps] freq to write energies to energy file nstxtcout = 500 ; [steps] freq to write coordinates to xtc trajectory xtc_precision = 1000 ; [real] precision to write xtc trajectory xtc_grps = System ; group(s) to write to xtc trajectory 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 = EnerPres ; 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 ; 7.3.14 Temperature Coupling tcoupl = nose-hoover ; temperature coupling with Nose-Hoover ensemble tc_grps = Protein Non-Protein ; groups to couple seperately to temperature bath tau_t = 0.1 0.1 ; [ps] time constant for coupling ref_t = 310 310 ; [K] reference temperature for coupling ; 7.3.15 Pressure Coupling pcoupl = parrinello-rahman ; pressure coupling where box vectors are variable pcoupltype = isotropic ; pressure coupling in x-y-z directions tau_p = 2.0 ; [ps] time constant for coupling compressibility = 4.5e-5 ; [bar^-1] compressibility ref_p = 1.0 ; [bar] reference pressure for coupling ; 7.3.17 Velocity Generation gen_vel = no ; velocity generation turned off ; 7.3.18 Bonds constraints = all-bonds ; convert all bonds to constraints constraint_algorithm = LINCS ; LINear Constraint Solver continuation = yes ; apply constraints to the start configuration lincs_order = 4 ; highest order in the expansion of the contraint coupling matrix lincs_iter = 1 ; number of iterations to correct for rotational lengthening lincs_warnangle = 30 ; [degrees] maximum angle that a bond can rotate before LINCS will complain