# ==============================
# Source the necessary Tcl files
# ==============================
# This depends on where and how NAMD is installed on your computer.
# Relative to the main NAMD directory, the appropriate file is
# /lib/namdcph/namdcph.tcl
#
source ../../lib/namdcph/namdcph.tcl

# ==================================
# These keywords all follow as usual
#
wrapWater      on
wrapAll        on
outputEnergies 5000
DCDFreq        5000

timestep           2.0
fullElectFrequency 1
rigidBonds         ALL
langevin           on
langevinTemp       298.0
langevinDamping    1.0
langevinHydrogen   no

switching         on
VDWForceSwitching on
LJCorrection      on
switchDist        10.0
cutoff            12.0
pairlistDist      14.0
exclude           scaled1-4
1-4scaling        1.0
PME               on
PMEGridSpacing    1.0

# ===============================================
# Begin constant-pH MD keywords and modifications
#
# Load force field files as usual, but add constant-pH specific parameters
set toppar_dir "../../toppar"
paratypecharmm on
parameters $toppar_dir/par_all36_prot.prm
parameters $toppar_dir/par_cph36_prot.prm
parameters $toppar_dir/par_all36_solvent.prm
# Load constant-pH specific topology files 
cphConfigFile $toppar_dir/conf_cph36_prot.json
topology      $toppar_dir/top_cph36_prot.rtf

# IMPORTANT! Note that, instead of the original PSF/PDB combination, we now
# reload a PSF/PDB that were generated as NAMD output. This accounts for
# modifications due to dummy atoms.
#

set pH 4.1
structure      $pH/ace_asp_nme_prod0.psf
coordinates    $pH/ace_asp_nme_prod0.pdb
binCoordinates $pH/ace_asp_nme_prod0.coor
binVelocities  $pH/ace_asp_nme_prod0.vel
extendedSystem $pH/ace_asp_nme_prod0.xsc
# NB - new restart file for constant-pH. This contains related settings, 
# including the pH. These will be overwritten by any new specifications here.
cphRestartFile $pH/ace_asp_nme_prod0.cphrst

outputname        $pH/ace_asp_nme_prod1
cphMDBasename     $pH/namdcph.md
cphSwitchBasename $pH/namdcph.sw

cphRun 500 5
exit