;;here no constraints and
; nslist=1 nstcomm removed as parameter
;notice that by default gromacs makes center of mass velocity removal
; here we are trying flexible spc to see if we get better energy consevation
;	User spoel (236)
;	Wed Nov  3 17:12:44 1993
;	Input file
;
title               =  Yo
cpp                 =  /lib/cpp
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  md
dt                  =  0.001	; ps !
nsteps              =  50000000	; 50 ns
;nstcomm             =  1 should not be there?
nstxout             =  50000
nstxtcout            =  1500
nstvout             =  50000
nstfout             =  0
nstlog              =  5000
nstenergy           =  1500
nstlist             =  1
ns_type             =  grid ;n-list parameter
rlist               =  1.0 ;cutoff for the short range neighbor list


; OPTIONS FOR ELECTROSTATICS AND VDW = 
; Method for doing electrostatics = 
coulombtype              = PME
; 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
ewald_geometry           = 3d
epsilon_surface          = 0
optimize_fft             = yes
; Nose-Hoover temperature coupling is off
Tcoupl              = no
tc-grps	            =
tau_t               =
ref_t               =
 Energy monitoring
energygrps	    =  Protein SOL Na
; Pressure coupling is off
Pcoupl              = no
Pcoupltype          = 
tau_p               = 
compressibility     = 
ref_p               = 
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529