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grompp_minim_noconstr.mdp
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grompp_minim_noconstr.mdp
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; GROMACS configuration for ...eGFP simulations
; virtual-sites NegCleGFP well-energy-conserving setup
; NPT simulation (amber99sb version and Slipids)
integrator = cg
tinit = 0
dt = 0.0001
nsteps = 1000
init_step = 0
; Energy minimization opts
emtol = 10
emstep = 0.0001
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10 ; number of correction steps for LBFGS
; ELECTRIC FIELD
; E-z = 1 +0.1 0
nstxout = 2000000 ;10ns
nstvout = 2000000 ;10ns
nstfout = 0
nstlog = 1000 ; 5ps
nstcalcenergy = 100 ; 0.5ps, default value=100 ; replex must be multiple of this value!
nstenergy = 1000 ; 5ps
nstxtcout = 100 ; 5ps
xtc-precision = 1000
xtc-grps =
energygrps = Protein ;Water_and_ions POPC
nstlist = 25 ; .05ps, Gromacs manual says values>20 give the best performance (for GPUs)
ns-type = grid ; grid search for neighbour list faster for larger sys. than simple
;Centre of mass movement removal
comm-mode = Linear
nstcomm = 100 ; 1.0ps, This should suffice
comm-grps =
;nstcheckpoint = 2000 ;10ps
; OPTIONS FOR ELECTROSTATICS AND VDW
cutoff-scheme = verlet ; group is alternative
coulombtype = PME ; Particle mesh Ewald, do not change
rcoulomb = 1.0 ; Real-space cut-off
vdwtype = cut-off
vdw-modifier = potential-shift-verlet ; =shifted-vdw with Verlet_cutoff_scheme, =none with grid_cutoff_scheme
rvdw = 1.0 ; VdW cut-off, orig paper rvdw=1.4, but this value is still fine (tested for both rigbonds an VSites, almost identical)
DispCorr = EnerPres ; Dispersion corrections to both the potential and pressure
table-extension = 1.0
fourierspacing = 0.12 ; PME grid
; Options no longer required with Verlet cut-off scheme
;rlist = 1.0 ; Short-range neighbor list
;rlistlong = 1.6 ; Long-range neighbor list
; OPTIONS FOR WEAK COUPLING ALGORITHMS
tcoupl = v-rescale ; Thermostat, v-rescale or nose-hoover is also fine
tc-grps = Protein ;POPC Water_and_ions ; Couple lipids and Water_and_ions seperatly
tau-t = 1.0 ;1.0 1.0 ; Time constant for temperature coupling
ref-t = 310 ;310 310 ; Desired temperature (K)
Pcoupl = parrinello-rahman ; Barostat
Pcoupltype = isotropic ; Pressure in xy and z couple separately
ref-p = 1.013 ; 1.013 ; Desired pressure (bar)
tau-p = 10.0 ;10.0 ; Time constant for pressure coupling
compressibility = 4.5e-5 ;4.5e-5 ; Same as for water
; CONSTRAINTS
constraints = none ;all-bonds
constraint-algorithm = Lincs
lincs-order = 10 ; Increasing these does not make much change to the precision of virtual sites (J. Melcr)
lincs-iter = 3 ; 5,2 conserves energy in NVE well enough (J. Melcr)
; Lambda-dynamics stuff
free-energy = no
;delta_lambda = 0.0 ; lambda won't change during simulation
;dhdl_derivatives = no
;nstdhdl = 0
; For Gromacs 4.6.+
;fep-lambdas = 0.000 0.092 0.183 0.271 0.358 0.441 0.522 0.597 0.669 0.734 0.794 0.849
;init-lambda-state = 0