;
;	File 'mdout.mdp' was generated
;	By user: xhuang (1000)
;	On host: huang
;	At date: Wed Jan 31 15:52:48 2007
;

; VARIOUS PREPROCESSING OPTIONS
title                    = Yo
; Preprocessor - specify a full path if necessary.
cpp                      = /lib/cpp
include                  = 
define                   = 

; RUN CONTROL PARAMETERS
integrator               = md
; Start time and timestep in ps
tinit                    = 0.0
dt                       = 0.000000001
nsteps                   = 0;
; 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                  = 1
; group(s) for center of mass motion removal
comm-grps                = 

; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
; Checkpointing helps you continue after crashes
nstcheckpoint            = 5000
; Output frequency for energies to log file and energy file
nstlog                   = 100
nstenergy                = 100
; Output frequency and precision for xtc file
nstxtcout                = 1000
xtc-precision            = 1000
; This selects the subset of atoms for the xtc file. You can
; select multiple groups. By default all atoms will be written.
xtc-grps                 = 


; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist                  = 1
; 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                    = 1.2

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype              = User ;Cut-off
rcoulomb-switch          = 0
rcoulomb                 = 1.2
; Relative dielectric constant for the medium and the reaction field
epsilon-r                = 1
epsilon_rf               = 1
; Method for doing Van der Waals
vdw-type                 = User
; cut-off lengths       
rvdw-switch              = 0
rvdw                     = 1.2

; Extension of the potential lookup tables beyond the cut-off
table-extension          = 0.15

;Selection of energy groups
energygrps               =  other
; Seperate tables between energy group pairs
energygrp_table          = 

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
Tcoupl                   = no ;berendsen
; Groups to couple separately
tc-grps                  = system
; Time constant (ps) and reference temperature (K)
tau_t                    = 0.1
ref_t                    = 300;50
; Pressure coupling     
Pcoupl                   = no
Pcoupltype               = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p                    = 0.5
compressibility          = 4.5e-5
ref_p                    = 1.0
; Random seed for Andersen thermostat
andersen_seed            = 815131

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no;yes
gen_temp                 = 300;50
gen_seed                 = 89689454


; ENERGY GROUP EXCLUSIONS
; Pairs of energy groups for which all non-bonded interactions are excluded
energygrp_excl           =  other other  other
constraints                      = none