;
;	User spoel (236)
;	Wed Nov  3 17:12:44 1993
;	Input file
;
title               =  YSun-md-9atom-try1 
cpp                 = c:\Progra~1\Gromacs\bin\cpp.exe
include             = 
define              = 
;cpp                 =  /lib/cpp
;define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  15000	; total 30 ps. this equals to dt x nsteps 
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              = no ; berendsen
tc-grps		  =  ;Protein	;SOL
tau_t               =  ;0.1	;0.1
ref_t               =  ;300	;300
; Energy monitoring
energygrps	    = polymer	;SOL

;- OPTIONS FOR ELECTROSTATICS AND VDW = 
;- Method for doing electrostatics = 
;coulombtype              = PME
;rcoulomb-switch          = 0
;rcoulomb                 = 1
;- Dielectric constant (DC) for cut-off or DC of reaction field = 
; epsilon-r                = 1
; Method for doing Van der Waals = 
vdw-type                 = Cut-off
; cut-off lengths        = 
rvdw-switch              = 0
rvdw                     = 1.0
; Apply long range dispersion corrections for Energy and Pressure = 
;DispCorr                 = EnerPres
; 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
;epsilon_surface          = 0
;optimize_fft             = no


; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  ;0.5
compressibility     =  ;4.5e-5
ref_p               =  ;1.0
; Pressure coupling      = 
;Pcoupl                   = Berendsen
;Pcoupltype               = isotropic 
; Time constant (ps), compressibility (1/bar) and reference P (bar) = 
;tau_p                    = 5.0		;5.0
;compressibility          = 4.5e-5 	      ;4.5e-5
;ref_p                    = 1.0		;1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
;non-equilibrium MD 
freezegrps          = botatom
freezedim           = Y Y Y
cos-acceleration    = 0
erergygrp_excl      =