MD scripts

em.mdp

; Define
define        = -DFLEXIBLE

; Run Control
integrator    = steep

; Energy Minimization
emtol        = 200.0
nsteps        = 5000

; Output Control
nstenergy    = 1
energygrps    = System

; Neighbor Searching
nstlist        = 1
ns_type        = grid
rlist        = 1.0

; PBC
pbc        = xyz

; Electrostatics
coulombtype    = PME
rcoulomb    = 1.0
pme_order    = 4
fourierspacing    = 0.16

; VdW
rvdw        = 1.0

; Bonds
constraints    = none
constraint_algorithm    = Lincs
unconstrained_start    = no
lincs_order    = 4
lincs_warnangle    = 30

nvt.mdp

; RUN CONTROL PARAMETERS
integrator    = md
dt        = 0.002
nsteps        = 5000000

; OUTPUT CONTROL OPTIONS
nstxout        = 500
nstvout        = 500
nstenergy    = 500
nstlog        = 500
nstxtcout    = 1000
xtc_precision    = 100
energygrps    = FAM
xtc-grps    = FAM

; NEIGHBORSEARCHING PARAMETERS
nstlist        = 5
ns_type        = grid
pbc        = xyz
rlist        = 1.0

; OPTIONS FOR ELECTROSTATIC AND VDW
coulombtype    = PME
rcoulomb    = 1.0
pme_order    = 4
fourierspacing    = 0.16
rvdw        = 1.0

; TEMPERATURE COUPLING
tcoupl        = v-rescale
tc-grps        = FAM 
tau_t        = 0.1
ref_t        = 300

; PRESSURE COUPLING
pcoupl        = no

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel        = yes
gen_temp    = 300
gen_seed    = -1

; OPTIONS FOR BOND CONSTRAINTS
constraints    = all-bonds
continuation    = no
constraint_algorithm    = Lincs
lincs_iter    = 1
lincs_order    = 4
lincs_warnangle    = 30

nvt.mdp

; RUN CONTROL PARAMETERS
integrator    = md
dt        = 0.002
nsteps        = 5000000

; OUTPUT CONTROL OPTIONS
nstxout        = 500
nstvout        = 500
nstenergy    = 500
nstlog        = 500
nstxtcout    = 1000
xtc_precision    = 100
energygrps    = FAM
xtc-grps    = FAM

; NEIGHBORSEARCHING PARAMETERS
nstlist        = 5
ns_type        = grid
pbc        = xyz
rlist        = 1.0

; OPTIONS FOR ELECTROSTATIC AND VDW
coulombtype    = PME
rcoulomb    = 1.0
pme_order    = 4
fourierspacing    = 0.16
rvdw        = 1.0

; TEMPERATURE COUPLING
tcoupl        = v-rescale
tc-grps        = FAM
tau_t        = 0.1
ref_t        = 300

; PRESSURE COUPLING
pcoupl        = Parrinello-Rahman
Pcoupltype    = Isotropic
tau_p        = 2.0
compressibility    = 4.5e-5
ref_p        = 1.0
refcoord_scaling    = com

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel        = no

; OPTIONS FOR BOND CONSTRAINTS
constraints    = all-bonds
continuation    = yes
constraint_algorithm    = Lincs
lincs_iter    = 1
lincs_order    = 4
lincs_warnangle    = 30

md_prod.mdp

; RUN CONTROL PARAMETERS
integrator    = md
dt        = 0.002
nsteps        = 5000000

; OUTPUT CONTROL OPTIONS
nstxout        = 1000
nstvout        = 1000
nstenergy    = 1000
nstlog        = 1000
nstxtcout    = 1000
xtc_precision    = 100
energygrps    = FAM
xtc-grps    = FAM

; NEIGHBORSEARCHING PARAMETERS
nstlist        = 5
ns_type        = grid
pbc        = xyz
rlist        = 1.0

; OPTIONS FOR ELECTROSTATIC AND VDW
coulombtype    = PME
rcoulomb    = 1.0
pme_order    = 4
fourierspacing    = 0.16
rvdw        = 1.0

; TEMPERATURE COUPLING
tcoupl        = v-rescale
tc-grps        = FAM
tau_t        = 0.1
ref_t        = 300

; PRESSURE COUPLING
pcoupl        = Parrinello-Rahman
Pcoupltype    = Isotropic
tau_p        = 2.0
compressibility    = 4.5e-5
ref_p        = 1.0
refcoord_scaling    = com

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel        = no

; OPTIONS FOR BOND CONSTRAINTS
constraints    = all-bonds
continuation    = yes
constraint_algorithm    = Lincs
lincs_iter    = 1
lincs_order    = 4
lincs_warnangle    = 30

;Dispersion Correction
DispCorr    = EnerPres