diff test-data/md.mdp @ 0:a81256d23782 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit a8eac146d0f6b9696f4afaaaa96891e8e324f78e"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/md.mdp	Tue Dec 21 13:45:19 2021 +0000
@@ -0,0 +1,50 @@
+
+                    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
+
+            
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