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Decrease cutoffs for faster simulations #1

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Decrease cutoffs for faster simulations #1

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71 changes: 71 additions & 0 deletions mdp_files/anneal.mdp
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Original file line number Diff line number Diff line change
@@ -0,0 +1,71 @@
;
; GROMACS
; Input for NVT anneal
;
;
define = -DPOSRES
integrator = md
nsteps = 125000 ; 250 ps
dt = 0.002
;
; Removing CM Translation and Rotation
comm_mode = Linear
nstcomm = 1000
;
; Output Control
nstlog = 1000
nstenergy = 1000
nstxout = 0
nstvout = 0
nstxtcout = 100
xtc_grps = Protein
nstfout = 0
;
; Neighbour Searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.0
;
; Electrostatic
rcoulomb = 1.0
coulombtype = pme
fourierspacing = 0.12
;periodic_molecules = yes
;
; VdW
vdw-type = shift
rvdw = 1.0
;
; Constraints
constraints = h-bonds
constraint-algorithm = lincs
lincs_iter = 4
;
; Temperature
Tcoupl = v-rescale
tc_grps = system
tau_t = 0.05
ref_t = 5
;
;
;; Simulated annealing
annealing = single ; single sequence of points for each T-coupling group (tc_grps = system)
annealing_npoints = 2 ; in this case two points - start and end temperatures
annealing_time = 0 240 ; time frame of heating - in this case heat over a period of 15 ps
annealing_temp = 5 298.15 ; start and end temperatures
;
;
; Pressure
Pcoupl = no
;Pcoupl = berendsen
;Pcoupltype = semiisotropic
;tau_p = 0.5 0.5
;compressibility = 0.0 4.5e-5
;ref_p = 0.0 1.0
;
; Initial Velocities
gen_vel = yes
gen_temp = 5
gen_seed = -1

48 changes: 27 additions & 21 deletions mdp_files/em.mdp
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Original file line number Diff line number Diff line change
@@ -1,28 +1,34 @@
;
; GROMACS
; Energy Minimization Script
; GROMACS
; Energy Minimization Script
;
;
define = -DFLEXIBLE ; pass to preprocessor
cpp = usr/bin/cpp ; location of preprocessor
constraints = none
integrator = steep ; steepest decents minimum (else cg)
nsteps = 10000
define = -DFLEXIBLE ; pass to preprocessor
cpp = usr/bin/cpp ; location of preprocessor
constraints = none
integrator = steep ; steepest decents minimum (else cg)
nsteps = 10000
;
; Energy Minimizing Stuff
; Energy Minimizing Stuff
;
emtol = 10 ; convergence total force(kJ/mol/nm) is smaller than
emstep = 0.01 ; initial step size (nm)
nstcomm = 100 ; frequency or COM motion removal
ns_type = grid
rlist = 1.4 ; cut-off distance for short range neighbors
rcoulomb = 1.4 ; distance for coulomb cut-off
coulombtype = PME ; electrostatics (Particle Mesh Ewald method)
fourierspacing = 0.12 ; max grid spacing when using PPPM or PME
vdw-type = Shift
rvdw = 1.2 ; VDW cut-off
Tcoupl = no ; temperature coupling
Pcoupl = no ; pressure coupling
gen_vel = no
emtol = 10 ; convergence total force(kJ/mol/nm) is smaller than
emstep = 0.01 ; initial step size (nm)
nstcomm = 100 ; frequency or COM motion removal
ns_type = grid
rlist = 1.0 ; cut-off distance for short range neighbors
rcoulomb = 1.0 ; distance for coulomb cut-off
coulombtype = PME ; electrostatics (Particle Mesh Ewald method)
fourierspacing = 0.12 ; max grid spacing when using PPPM or PME
vdw-type = Shift
rvdw = 1.0 ; VDW cut-off
Tcoupl = no ; temperature coupling
Pcoupl = no ; pressure coupling
gen_vel = no

; Freeze Groups
;freezegrps = AlkChain
;freezedim = N N Y
;energygrps = AlkChain
;energygrp_excl = AlkChain AlkChain


45 changes: 28 additions & 17 deletions mdp_files/npt_equil.mdp
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,8 @@
;
;define = -DPOSRES
integrator = md
nsteps = 5000000
nsteps = 500000 ; 1 ns total
nstcalcenergy = 1000 ; set to 1 for PLUMED sims in WTE
dt = 0.002
;
; Removing CM Translation and Rotation
Expand All @@ -20,24 +21,31 @@ nstvout = 0
nstxtcout = 1000
nstfout = 0
;
; Group Definition
xtc-precision = 5000
xtc-grps = System
;
; Neighbour Searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
rlist = 1.0
;
; Electrostatic
rcoulomb = 1.4
rcoulomb = 1.0
coulombtype = pme
fourierspacing = 0.12
;periodic_molecules = yes
;
; VdW
vdw-type = shift
rvdw = 1.2
; Van der Waals
vdw-type = Cut-off
vdw_modifier = Force-switch
rvdw = 1.0
rvdw-switch = 0.9
cutoff-scheme = Verlet
;
; Constraints
constraints = h-bonds
constraints = all-bonds
constraint-algorithm = lincs
lincs_iter = 4
;
Expand All @@ -47,15 +55,18 @@ tc_grps = system
tau_t = 0.1
ref_t = 298.15
;
; Initial Velocities
gen_vel = yes
continuation = no
gen_temp = 298.15
gen_seed = -1
;
; Pressure
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
Pcoupl = no
;Pcoupl = berendsen
;Pcoupltype = semiisotropic
;tau_p = 1.0
;compressibility = 4.5e-5
;ref_p = 1.0
;
;
; Initial Velocities
gen_vel = yes
gen_temp = 298.15
gen_seed = -1

32 changes: 21 additions & 11 deletions mdp_files/npt_prod.mdp
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,8 @@
;
;define = -DPOSRES
integrator = md
nsteps = 10000000
nsteps = 10000000 ; 20 ns total
nstcalcenergy = 1000
dt = 0.002
;
; Removing CM Translation and Rotation
Expand All @@ -20,24 +21,31 @@ nstvout = 0
nstxtcout = 1000
nstfout = 0
;
; Group Definition
xtc-precision = 5000
xtc-grps = System
;
; Neighbour Searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
rlist = 1.0
;
; Electrostatic
rcoulomb = 1.4
rcoulomb = 1.0
coulombtype = pme
fourierspacing = 0.12
;periodic_molecules = yes
;
; VdW
vdw-type = shift
rvdw = 1.2
; Van der Waals
vdw-type = Cut-off
vdw_modifier = Force-switch
rvdw = 1.0
rvdw-switch = 0.9
cutoff-scheme = Verlet
;
; Constraints
constraints = h-bonds
constraints = all-bonds
constraint-algorithm = lincs
lincs_iter = 4
;
Expand All @@ -47,15 +55,17 @@ tc_grps = system
tau_t = 0.1
ref_t = 298.15
;
; Initial Velocities
continuation = yes
gen_vel = no
;gen_temp = 298.15
;gen_seed = -1
;
; Pressure
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
;
; Initial Velocities
gen_vel = yes
gen_temp = 298.15
gen_seed = -1

49 changes: 29 additions & 20 deletions mdp_files/nvt_equil.mdp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,8 @@
;
;define = -DPOSRES
integrator = md
nsteps = 5000000
nsteps = 500000 ; 1 ns total
nstcalcenergy = 1000 ; set to 1 for PLUMED sims in WTE
dt = 0.002
;
; Removing CM Translation and Rotation
Expand All @@ -14,30 +15,37 @@ nstcomm = 1000
;
; Output Control
nstlog = 1000
nstenergy = 1000
nstenergy = 100
nstxout = 0
nstvout = 0
nstxtcout = 100
nstxtcout = 1000
nstfout = 0
;
; Group Definition
xtc-precision = 5000
xtc-grps = System
;
; Neighbour Searching
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
rlist = 1.0
;
; Electrostatic
rcoulomb = 1.4
rcoulomb = 1.0
coulombtype = pme
fourierspacing = 0.12
;periodic_molecules = yes
;
; VdW
vdw-type = shift
rvdw = 1.2
; Van der Waals
vdw-type = Cut-off
vdw_modifier = Force-switch
rvdw = 1.0
rvdw-switch = 0.9
cutoff-scheme = Verlet
;
; Constraints
constraints = h-bonds
constraints = all-bonds
constraint-algorithm = lincs
lincs_iter = 4
;
Expand All @@ -47,16 +55,17 @@ tc_grps = system
tau_t = 0.1
ref_t = 298.15
;
; Initial Velocities
gen_vel = yes
continuation = no
gen_temp = 298.15
gen_seed = -1
;
; Pressure
Pcoupl = no
;Pcoupl = berendsen
;Pcoupltype = semiisotropic
;tau_p = 0.5 0.5
;compressibility = 0.0 4.5e-5
;ref_p = 0.0 1.0
Pcoupl = berendsen ; parrinello-rahman berendsen (for equilibration only)
Pcoupltype = isotropic
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
;
;
; Initial Velocities
gen_vel = yes
gen_temp = 298.15
gen_seed = -1

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