;	By user: pcl
; VARIOUS PREPROCESSING OPTIONS
title                    = Yo
cpp                      = /lib/cpp
include                  = 
define                   = 

; RUN CONTROL PARAMETERS
integrator               = bd
; Start time and timestep in ps
tinit                    = 0
dt                       = 0.00001
nsteps                   = 100000000
                    
comm-mode                = Linear
nstcomm                  = 1
comm-grps                = System

; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric                  = 0.005
ld_seed                  = 1993


; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol                    = 10
emstep                   = 0.1

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 1000
nstvout                  = 1000
nstfout                  = 0

; Output frequency for energies to log file and energy file
nstlog                   = 1000
nstenergy                = 1000
; Output frequency and precision for xtc file
nstxtcout                = 1000
xtc-precision            = 1000

; 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                    = 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = PME
rcoulomb-switch          = 0
rcoulomb                 = 0.9
; Relative dielectric constant for the medium and the reaction field
epsilon_r                = 13.89354;   
; Method for doing Van der Waals
vdw-type                 = Cut-off      
rvdw-switch              = 0
rvdw                     = 0.9

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
Tcoupl                   = Berendsen
; Groups to couple separately
tc-grps                  = NA POL
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.01 0.01
ref_t                    = 120.2717 120.2717; 

; Pressure coupling     
Pcoupl                   = no

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no

; OPTIONS FOR BONDS    
constraints              = none