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35 lines
1.8 KiB
35 lines
1.8 KiB
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define = -DFLEXIBLE |
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integrator = md ; leap-frog integrator |
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nsteps = 1000 ; 1 * 500000 = 50 ps |
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dt = 0.001 ; 0.5 fs |
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nstxout = 100 ; save coordinates every 1.0 ps |
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nstenergy = 100 ; save energies every 1.0 ps |
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nstlog = 100 ; update log file every 1.0 ps |
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; Bond parameters |
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continuation = no ; first dynamics run |
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constraint_algorithm = lincs ; holonomic constraints |
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constraints = h-bonds ; bonds involving H are constrained |
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lincs_iter = 1 ; accuracy of LINCS |
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lincs_order = 4 ; also related to accuracy |
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; Nonbonded settings |
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cutoff-scheme = Verlet ; Buffered neighbor searching |
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ns_type = grid ; search neighboring grid cells |
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nstlist = 10 ; 20 fs, largely irrelevant with Verlet |
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rcoulomb = 0.9613990804113833 ; short-range electrostatic cutoff (in nm) |
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rvdw = 0.9613990804113833 ; short-range van der Waals cutoff (in nm) |
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DispCorr = EnerPres ; account for cut-off vdW scheme |
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; Electrostatics |
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coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics |
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pme_order = 4 ; cubic interpolation |
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fourierspacing = 0.16 ; grid spacing for FFT |
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; Temperature coupling is off |
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tcoupl = no ; no temperature coupling in NVE |
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; Pressure coupling is off |
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pcoupl = no ; no pressure coupling in NVE |
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; Periodic boundary conditions |
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pbc = xyz ; 3-D PBC |
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; Velocity generation |
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gen_vel = no ; Velocity generation is off |
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