Add full test dataset

testdata/mdps/em.mdp

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+; em.mdp - used as input into grompp to generate em.tpr
+; Parameters describing what to do, when to stop and what to save
+integrator  = steep         ; Algorithm (steep = steepest descent minimization)
+emtol       = 1000.0        ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
+emstep      = 0.01          ; Minimization step size
+nsteps      = 5000          ; Fast test: max minimization steps
+
+; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
+nstlist         = 1         ; Frequency to update the neighbor list and long range forces
+cutoff-scheme   = Verlet    ; Buffered neighbor searching
+ns_type         = grid      ; Method to determine neighbor list (simple, grid)
+coulombtype     = PME       ; Treatment of long range electrostatic interactions
+rcoulomb        = 1.0       ; Short-range electrostatic cut-off
+rvdw            = 1.0       ; Short-range Van der Waals cut-off
+pbc             = xyz       ; Periodic Boundary Conditions in all 3 dimensions

testdata/mdps/md.mdp

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+title                   = OPLS Lysozyme MD run 
+; Run parameters
+integrator              = md        ; leap-frog integrator
+nsteps                  = 25000     ; Fast test: 50 ps
+dt                      = 0.002     ; 2 fs
+; Output control
+nstxout                 = 0         ; suppress bulky .trr file by specifying 
+nstvout                 = 0         ; 0 for output frequency of nstxout,
+nstfout                 = 0         ; nstvout, and nstfout
+nstenergy               = 1000      ; save energies every 2.0 ps
+nstlog                  = 1000      ; update log file every 2.0 ps
+nstxout-compressed      = 1000      ; save compressed coordinates every 2.0 ps
+compressed-x-grps       = System    ; save the whole system
+; Bond parameters
+continuation            = yes       ; Restarting after NPT 
+constraint_algorithm    = lincs     ; holonomic constraints 
+constraints             = h-bonds   ; bonds involving H 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        ; 20 fs, largely irrelevant with Verlet scheme
+; vdW
+rvdw                    = 1.2       ; short-range van der Waals cutoff (in nm)
+rvdw-switch             = 1.0
+vdw-modifier            = force-switch
+DispCorr                = No
+; Electrostatics
+rcoulomb                = 1.2       ; short-range electrostatic cutoff (in nm)
+coulombtype             = PME       ; Particle Mesh Ewald for long-range electrostatics
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.16      ; grid spacing for FFT
+; Temperature coupling is on
+tcoupl                  = V-rescale             ; modified Berendsen thermostat
+tc-grps                 = System 
+tau_t                   = 1.0
+ref_t                   = 298 
+; Pressure coupling is on
+pcoupl                  = C-rescale 
+pcoupltype              = isotropic             ; uniform scaling of box vectors
+tau_p                   = 5.0                   ; time constant, in ps
+ref_p                   = 1.0                   ; reference pressure, in bar
+compressibility         = 4.5e-5                ; isothermal compressibility of water, bar^-1
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+; Velocity generation
+gen_vel                 = no        ; Velocity generation is off 

testdata/mdps/npt.mdp

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+title                   = OPLS Lysozyme NPT equilibration 
+define                  = -DPOSRES  ; position restrain the protein
+; Run parameters
+integrator              = md        ; leap-frog integrator
+nsteps                  = 10000     ; Fast test: 20 ps
+dt                      = 0.002     ; 2 fs
+; Output control
+nstxout                 = 1000      ; save coordinates every 2.0 ps
+nstvout                 = 1000      ; save velocities every 2.0 ps
+nstenergy               = 1000      ; save energies every 2.0 ps
+nstlog                  = 1000      ; update log file every 2.0 ps
+; Bond parameters
+continuation            = yes       ; Restarting after NVT 
+constraint_algorithm    = lincs     ; holonomic constraints 
+constraints             = h-bonds   ; bonds involving H 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        ; 20 fs, largely irrelevant with Verlet scheme
+; vdW
+rvdw                    = 1.2       ; short-range van der Waals cutoff (in nm)
+rvdw-switch             = 1.0
+vdw-modifier            = force-switch
+DispCorr                = No
+; Electrostatics
+rcoulomb                = 1.2       ; short-range electrostatic cutoff (in nm)
+coulombtype             = PME       ; Particle Mesh Ewald for long-range electrostatics
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.16      ; grid spacing for FFT
+; Temperature coupling is on
+tcoupl                  = V-rescale ; stochastic Bussi thermostat
+tc-grps                 = System 
+tau_t                   = 1.0
+ref_t                   = 298 
+; Pressure coupling is on
+pcoupl                  = C-rescale 
+pcoupltype              = isotropic             ; uniform scaling of box vectors
+tau_p                   = 5.0                   ; time constant, in ps
+ref_p                   = 1.0                   ; reference pressure, in bar
+compressibility         = 4.5e-5                ; isothermal compressibility of water, bar^-1
+refcoord_scaling        = com
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+; Velocity generation
+gen_vel                 = no        ; Velocity generation is off 

testdata/mdps/nvt.mdp

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+title                   = OPLS Lysozyme NVT equilibration 
+define                  = -DPOSRES  ; position restrain the protein
+; Run parameters
+integrator              = md        ; leap-frog integrator
+nsteps                  = 10000     ; Fast test: 20 ps
+dt                      = 0.002     ; 2 fs
+; Output control
+nstxout                 = 1000      ; save coordinates every 2.0 ps
+nstvout                 = 1000      ; save velocities every 2.0 ps
+nstenergy               = 1000      ; save energies every 2.0 ps
+nstlog                  = 1000      ; update log file every 2.0 ps
+; Bond parameters
+continuation            = no        ; first dynamics run
+constraint_algorithm    = lincs     ; holonomic constraints 
+constraints             = h-bonds   ; bonds involving H 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        ; 20 fs, largely irrelevant with Verlet
+; vdW
+rvdw                    = 1.2       ; short-range van der Waals cutoff (in nm)
+rvdw-switch             = 1.0
+vdw-modifier            = force-switch
+DispCorr                = No        ; per CHARMM FF convention 
+; Electrostatics
+rcoulomb                = 1.2       ; short-range electrostatic cutoff (in nm)
+coulombtype             = PME       ; Particle Mesh Ewald for long-range electrostatics
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.16      ; grid spacing for FFT
+; Temperature coupling is on
+tcoupl                  = V-rescale ; stochastic Bussi thermostat 
+tc-grps                 = System 
+tau_t                   = 1.0       ; value of tau (ps)
+ref_t                   = 298       ; temperature (K) 
+; Pressure coupling is off
+pcoupl                  = no        ; no pressure coupling in NVT
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+; Velocity generation
+gen_vel                 = yes       ; assign velocities from Maxwell distribution
+gen_temp                = 298       ; temperature for Maxwell distribution
+gen_seed                = -1        ; generate a random seed

testdata/samplesheet/v1.0/samplesheet_test_full.csv

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+sample,structure,em_mdp,nvt_mdp,npt_mdp,md_mdp,forcefield,box_type,distance_to_box
+LYSOZYME_1AKI,https://raw.githubusercontent.com/nf-core/test-datasets/moleculardynamics/testdata/experimental_structures/1AKI.pdb,https://raw.githubusercontent.com/nf-core/test-datasets/moleculardynamics/testdata/mdps/em.mdp,https://raw.githubusercontent.com/nf-core/test-datasets/moleculardynamics/testdata/mdps/nvt.mdp,https://raw.githubusercontent.com/nf-core/test-datasets/moleculardynamics/testdata/mdps/npt.mdp,https://raw.githubusercontent.com/nf-core/test-datasets/moleculardynamics/testdata/mdps/md.mdp,charmm27,cubic,1.0