# NAMD configuration file for heating
# based on BPTI example in NAMD manual and apoa1.namd.
# modified by ssomani on 24 Aug, 2004
# modified by ssomani on 01 Sep, 2004 -- added MOL

######################TOSET############################
# molecular system
set MOL            2sol
structure          ${MOL}.psf

# after minimization
set inprot       ${MOL}_min
coordinates      ${inprot}.coor
velocities       ${inprot}.vel
extendedSystem   ${inprot}.xsc

#restart previous heat run
#coordinates kin_heat.coor
#velocities  kin_heat.vel
#extendedSystem kin_heat.xsc

set outputname     ${MOL}_heat
set heat_restart   ${MOL}_heat_restart

set desiredtemp    300       ;# initial temperature

puts "this will go into the log file. ${inprot}.coor"
######################TOSET############################

# start from 0 for heating.
# use only coordinates after em, but not velocities.

# force field
paratypecharmm on
parameters par_all22_prot.inp 
exclude scaled1-4
1-4scaling 1.0

wrapAll on

PME on
PMEGridSizeX 64 # size along cellBasisVector1.
PMEGridSizeY 64 # along cellBasisVector2.
PMEGridSizeZ 64 
# use numbers with small integer factors: 2,3,5.

# approximations
switching on
switchdist 10
cutoff 12
pairlistdist 13.5

# center-of-mass motion is automatically removed.

# integrator
timestep      2.0  # in fs.
stepspercycle 20
nonbondedFreq 2 # BerendsenPressureFreq takes this value.

# output
outputName          $outputname

dcdfreq             100     ;# how often we output trajectories
xstFreq             100
outputEnergies      100
outputPressure      100
outputtiming        100
binaryoutput        no

# for restarting:
restartname         $heat_restart
restartfreq         1000
restartsave         yes
binaryrestart       no     ;# preserves more accuracy.

#temperature 0  # sets initial temperature. use '; #' aft "run".
# disable 'temperature' when using a velocity file.

# For heating, use temperature reassignment.
#reassignFreq 300  # tuned to be suit 'natural' heating for system.
#reassignTemp 0	  # to start from 0 Kelvin, else always lagging by 25K.
#reassignIncr 25 
#reassignHold 300

langevin         on
langevinTemp     $desiredtemp
langevinDamping  1.0 # mailing-list
langevinHydrogen on


run 7000 ; # heat for 7 ps