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- title = Protein-ligand complex NVT equilibration
- define = -DPOSRES ; position restrain the protein and ligand
- ; Run parameters
- integrator = md ; leap-frog integrator
- nsteps = 50000 ; 2 * 50000 = 100 ps
- dt = 0.002 ; 2 fs
- ; Output
- nstxout = 500 ; save coordinates every 1.0 ps
- nstvout = 500 ; save velocities every 1.0 ps
- nstenergy = 500 ; save energies every 1.0 ps
- nstlog = 500 ; update log file every 1.0 ps
- energygrps = Protein DNA
- ; Bond
- continuation = no ; first dynamics run
- constraint_algorithm = lincs ; holonomic constraints
- constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
- lincs_iter = 1 ; accuracy of LINCS
- lincs_order = 4 ; also related to accuracy
- ; Neighborsearching
- cutoff-scheme = Verlet
- ns_type = grid ; search neighboring grid cells
- nstlist = 20 ; 20 fs, largely irrelevant with Verlet
- rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
- rvdw = 1.2 ; short-range VdW cutoff
- ; Electrostatics
- coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
- pme_order = 4 ; cubic interpolation
- fourierspacing = 0.16 ; grid spacing for FFT
- ; Temperature coupling
- tcoupl = V-rescale ; modified Berendsen thermostat
- tc-grps = Protein_DNA Water_and_ions ; two coupling groups - more accurate
- tau_t = 0.1 0.1 ; time constant, in ps
- ref_t = 300 300 ; reference temperature, one for each group, in K
- ; Pressure coupling
- pcoupl = no ; no pressure coupling in NVT
- ; Periodic boundary conditions
- pbc = xyz ; 3-D PBC
- ; Dispersion correction
- DispCorr = EnerPres ; account for cut-off vdW scheme
- ; Velocity generation
- gen_vel = yes ; assign velocities from Maxwell distribution
- gen_temp = 300 ; temperature for Maxwell distribution
- gen_seed = -1 ; generate a random seed
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