diff --git a/scripts/gromacs/mdp/ions.mdp b/scripts/gromacs/mdp/ions.mdp new file mode 100644 index 0000000..eb2cfc5 --- /dev/null +++ b/scripts/gromacs/mdp/ions.mdp @@ -0,0 +1,15 @@ +; ions.mdp - used as input into grompp to generate ions.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 = 50000 ; Maximum number of (minimization) steps to perform + +; 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 = cutoff ; 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 diff --git a/scripts/gromacs/mdp/md.mdp b/scripts/gromacs/mdp/md.mdp new file mode 100644 index 0000000..75080d1 --- /dev/null +++ b/scripts/gromacs/mdp/md.mdp @@ -0,0 +1,46 @@ +title = OPLS Lysozyme NPT equilibration +; Run parameters +integrator = md ; leap-frog integrator +nsteps = 500000 ; 2 * 500000 = 1000 ps (1 ns) +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 = 5000 ; save energies every 10.0 ps +nstlog = 5000 ; update log file every 10.0 ps +nstxout-compressed = 5000 ; save compressed coordinates every 10.0 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 +; Neighborsearching +cutoff-scheme = Verlet ; Buffered neighbor searching +ns_type = grid ; search neighboring grid cells +nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme +rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) +rvdw = 1.0 ; short-range van der Waals cutoff (in nm) +; Electrostatics +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 = 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 +; 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 +; 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 diff --git a/scripts/gromacs/mdp/minim.mdp b/scripts/gromacs/mdp/minim.mdp new file mode 100644 index 0000000..1af4f96 --- /dev/null +++ b/scripts/gromacs/mdp/minim.mdp @@ -0,0 +1,15 @@ +; minim.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 = 50000 ; Maximum number of (minimization) steps to perform + +; 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 diff --git a/scripts/gromacs/mdp/npt.mdp b/scripts/gromacs/mdp/npt.mdp new file mode 100644 index 0000000..eca4d72 --- /dev/null +++ b/scripts/gromacs/mdp/npt.mdp @@ -0,0 +1,44 @@ +title = OPLS Lysozyme NPT equilibration +; define = -DPOSRES ; position restrain the protein +; Run parameters +integrator = md ; leap-frog integrator +nsteps = 50000 ; 2 * 50000 = 100 ps +dt = 0.002 ; 2 fs +; Output control +nstxout = 500 ; save coordinates every 1.0 ps +nstvout = 500 ; save velocities every 1.0 ps +nstenergy = 500 ; save energies every 1.0 ps +nstlog = 500 ; update log file every 1.0 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 +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 = 0.16 ; 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 +; 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 +refcoord_scaling = com +; Periodic boundary conditions +pbc = xyz ; 3-D PBC +; Velocity generation +gen_vel = no ; Velocity generation is off diff --git a/scripts/gromacs/mdp/nvt.mdp b/scripts/gromacs/mdp/nvt.mdp new file mode 100644 index 0000000..5aaec44 --- /dev/null +++ b/scripts/gromacs/mdp/nvt.mdp @@ -0,0 +1,41 @@ +title = OPLS Lysozyme NVT equilibration +;define = -DPOSRES ; position restrain the protein +; Run parameters +integrator = md ; leap-frog integrator +nsteps = 50000 ; 2 * 50000 = 100 ps +dt = 0.002 ; 2 fs +; Output control +nstxout = 500 ; save coordinates every 1.0 ps +nstvout = 500 ; save velocities every 1.0 ps +nstenergy = 500 ; save energies every 1.0 ps +nstlog = 500 ; update log file every 1.0 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 +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 = 0.16 ; 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 +; 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 = 300 ; temperature for Maxwell distribution +gen_seed = -1 ; generate a random seed diff --git a/scripts/gromacs/mdp/prod.mdp b/scripts/gromacs/mdp/prod.mdp new file mode 100644 index 0000000..0f6ea32 --- /dev/null +++ b/scripts/gromacs/mdp/prod.mdp @@ -0,0 +1,41 @@ +title = OPLS Lysozyme NVT equilibration +;define = -DPOSRES ; position restrain the protein +; Run parameters +integrator = md ; leap-frog integrator +nsteps = 2500000 ; 2fs * 125000000 steps = 250 ns +dt = 0.002 ; 2 fs +; Output control +nstxout = 10000 ; save coordinates every 1.0 ps +nstvout = 10000 ; save velocities every 1.0 ps +nstenergy = 10000 ; save energies every 1.0 ps +nstlog = 10000 ; update log file every 1.0 ps +; Bond parameters +continuation = yes ; 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 +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 = 0.16 ; 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 = 300.00 300.00 ; reference temperature, one for each group, in 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 = 300.00 ; temperature for Maxwell distribution +;gen_seed = -1 ; generate a random seed