annotate test-data/md.mdp @ 3:b01f3db44534 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 5536c9fbb2f680a5f296db81362099e5a68e0587"

                    title    = OPLS Lysozyme MD simulation 
                    ; Run parameters
                    integrator  = md    ; leap-frog integrator
                    nsteps    = 500  ; 2 * 500000 = 1000 ps (1 ns)
                    dt        = 0.002    ; 2 fs
                    ; Output control
                    nstxout            = 50    ; save coordinates every 10.0 ps
                    nstvout            = 50    ; save velocities every 10.0 ps
                    nstenergy          = 50    ; save energies every 10.0 ps
                    nstlog            = 50    ; update log file every 10.0 ps
                    nstxout-compressed  = 50      ; save compressed coordinates every 10.0 ps
                                                    ; nstxout-compressed replaces nstxtcout
                    compressed-x-grps   = System    ; group(s) to write to the compressed trajectory file
                    ; Bond parameters
                    continuation          = yes    ; Restarting after NPT 
                    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        = 10      ; 20 fs, largely irrelevant with Verlet scheme
                    rcoulomb      = 1.0    ; Short-range electrostatic cut-off
                    rlist       = 1.0 ; Cut-off distance for the short-range neighbor list.
                    rvdw        = 1.0    ; Short-range Van der Waals cut-off
                    ; Electrostatics
                    coulombtype      = PME    ; method for electrostatics calculations e.g. PME
                    pme_order      = 4        ; cubic interpolation
                    fourierspacing  = 0.16    ; grid spacing for FFT
                    ; Temperature coupling is on
                    tcoupl    = V-rescale              ; modified Berendsen thermostat
                    tc-grps    = Protein Non-Protein  ; 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
                    ; Periodic boundary conditions
                    pbc    = xyz    ; 3-D PBC
                    ; Dispersion correction
                    DispCorr  = EnerPres  ; account for cut-off vdW scheme
                    ; Velocity generation
                    gen_vel    = no    ; Velocity generation is off
                    ; Pressure coupling is on
                    pcoupl            = Parrinello-Rahman      ; Pressure coupling on in NPT
                    pcoupltype          = isotropic              ; uniform scaling of box vectors
                    tau_p            = 2.0                ; time constant, in ps
                    ref_p            = 1.0                ; reference pressure, in bar
                    compressibility     = 4.5e-5              ; isothermal compressibility of water, bar^-1