grompp-NPT.mdp

; VARIOUS PREPROCESSING OPTIONS
; Preprocessor - specify a full path if necessary.
include                  = 
define                   = 

; RUN CONTROL PARAMETERS
integrator               = sd 
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.020
nsteps                   = 1000000
; For exact run continuation or redoing part of a run
init_step                = 0
; mode for center of mass motion removal
comm-mode                = Linear
; number of steps for center of mass motion removal
nstcomm                  = 10
; group(s) for center of mass motion removal
comm_grps                = 
;system

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
ld-seed                  = -1

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
; Output frequency for energies to log file and energy file
nstlog                   = 100
nstenergy                = 100
; Output frequency and precision for xtc file
nstxout-compressed       = 100
compressed-x-precision   = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
compressed-x-grps        = System ;Protein 
; Selection of energy groups
energygrps               = VNL EST C1 NO 

; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 10
; ns algorithm (simple or grid)
ns_type                  = grid
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc                      = xyz
; nblist cut-off        
rlist                    = 1.5


; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = Cut-off 
rcoulomb-switch          = 0
rcoulomb                 = 1.5
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 1
epsilon_rf               = 1
; Method for doing Van der Waals
vdwtype                  = user
; cut-off lengths       
rvdw-switch              = 0
rvdw                     = 1.5
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                 = EnerPres 
; Extension of the potential lookup tables beyond the cut-off
table-extension          = 1.0
; Seperate tables between energy group pairs
energygrp_table          = VNL VNL VNL EST VNL C1 VNL NO EST EST EST C1 EST NO C1 C1 C1 NO NO NO
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters
pme_order                = 4
ewald_rtol               = 1e-05
ewald_geometry           = 3d
epsilon_surface          = 0

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
tcoupl                   = berendsen
; Groups to couple separately
tc-grps                  = System
; Time constant (ps) and reference temperature (K)
tau_t                    = 1.0
ref_t                    = 300
; Pressure coupling     
Pcoupl                   = berendsen
pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 2.0
compressibility          = 4.5e-5
ref_p                    = 1.0


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

; OPTIONS FOR BONDS    
constraints              = none
; Type of constraint algorithm
constraint_algorithm     = LINCS
; Use successive overrelaxation to reduce the number of shake iterations
Shake-SOR                = no
; Relative tolerance of shake
shake-tol                = 1e-04
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 4
; Number of iterations in the final step of LINCS. 1 is fine for
; normal simulations, but use 2 to conserve energy in NVE runs.
; For energy minimization with constraints it should be 4 to 8.
lincs_iter               = 2
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle          = 30
; Convert harmonic bonds to morse potentials
morse                    = no

; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl           = 

cutoff-scheme = Group