imdclient 0.1.0__py3-none-any.whl

imdclient/data/gromacs/md/gromacs_v3_nst1.mdp

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+title                   = PRODUCTION IN NPT
+ld-seed                 = 1
+; Run parameters
+integrator              = md        ; leap-frog integrator
+nsteps                  = 100    ; 1 * 1000 = 1 ps
+dt                      = 0.001     ; 1 fs
+; Output control
+nstxout                 = 1      ; save coordinates every 1 fs
+nstvout                 = 1      ; save velocities every 1 fs
+nstfout                 = 1
+nstenergy               = 1      ; save energies every 1 fs
+nstlog                  = 10      ; update log file every 1 ps
+; Center of mass (COM) motion
+nstcomm                 = 10        ; remove COM motion every 10 steps
+comm-mode               = Linear    ; remove only COM translation (liquids in PBC) 
+; Bond parameters
+continuation            = yes       ; first dynamics run
+constraint_algorithm    = lincs     ; holonomic constraints
+constraints             = all-bonds ; all bonds lengths are constrained
+lincs_iter              = 1         ; accuracy of LINCS
+lincs_order             = 4         ; also related to accuracy
+; Nonbonded settings
+cutoff-scheme           = Verlet    ; Buffered neighbor searching
+ns_type                 = grid      ; search neighboring grid cells
+nstlist                 = 10        ; 10 fs, largely irrelevant with Verlet
+rcoulomb                = 1.0       ; short-range electrostatic cutoff (in nm)
+rvdw                    = 1.0       ; short-range van der Waals cutoff (in nm)
+DispCorr                = EnerPres  ; account for cut-off vdW scheme
+; Electrostatics
+coulombtype             = PME       ; Particle Mesh Ewald for long-range electrostatics
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.12      ; grid spacing for FFT
+; Temperature coupling is on
+tcoupl                  = Nose-Hoover       ; good for production, after equilibration
+; we define separate thermostats for the solute and solvent (need to adapt)
+; see default groups defined by Gromacs for your system or define your own (make_ndx)
+tc-grps                 = Protein  SOL      ; the separate groups for the thermostats
+tau-t                   = 1.0      1.0      ; time constants for thermostats (ps)
+ref-t                   = 300      300      ; reference temperature for thermostats (K)
+; Pressure coupling is off
+pcoupl                  = Parrinello-Rahman ; good for production, after equilibration
+tau-p                   = 2.0               ; time constant for barostat (ps)
+compressibility         = 4.5e-5            ; compressibility (1/bar) set to water at ~300K
+ref-p                   = 1.0               ; reference pressure for barostat (bar)
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+; Velocity generation
+gen_vel                 = no
+IMD-group               = System
+IMD-nst                 = 1
+IMD-version             = 3
+IMD-time                = yes
+IMD-box                 = yes
+IMD-coords              = yes
+IMD-unwrap              = no
+IMD-vels                = yes
+IMD-forces              = yes
+IMD-energies            = no