# NAMD Config file - autogenerated by NAMDgui plugin
# Author: Jan Saam,  saam@charite.de

# input
coordinates             lip-only_autopsf.pdb
structure               lip-only_autopsf.psf
parameters              par_all27_prot_lipid_na.inp
paratypecharmm          on

# output
set output              lip-only_autopsf
outputname              $output
dcdfile                 ${output}.dcd
xstFile                 ${output}.xst
dcdfreq                 50
xstFreq                 50

binaryoutput            no
binaryrestart           no
outputEnergies          100
restartfreq             1000

# mobile atom selection:
# all and not backbone
fixedAtoms              on
fixedAtomsFile          lip-only_autopsf_fixed.pdb
fixedAtomsCol           O

# Force field parameters
exclude                 scaled1-4
1-4scaling              1
cutoff                  12
switching               On
switchdist              10
pairlistdist            14

# Multiple timestepping
firsttimestep           0
timestep                1
stepspercycle           20
nonbondedFreq           2
fullElectFrequency      4

# Temperature control

set temperature         310
temperature             $temperature;  # initial temperature


# Scripting

tclforces on
tclforcesScript { 

set at1 1300
set at2 4618
addatom $at1
addatom $at2

set k  100.0
set r0 5.907

print " TCLFORCE ACTION "


proc calcforces {} {

 global  at1 at2 k r0 
 loadcoords c

 set r12 [vecsub $c($at2) $c($at1) ]  
 
 set r   [veclength $r12 ]
 
 set n0  [vecnorm $r12]
 
 set force [expr $k*($r-$r0)]
 
 set f1 [vecscale  $force $n0 ]
 set f2 [vecscale -$force $n0 ]

 addforce $at1 $f1
 addforce $at2 $f2

}

# Returns: the vector length
proc veclength {v} {

 set retval 0
 foreach term $v {
         set retval [expr $retval + $term * $term ]
                 }
 return [expr sqrt($retval)]

}

# Returns: the normal vector
proc vecnorm {v} {
 set sum 0
 foreach term $v {
         set sum [expr $sum + $term*$term]
                 }
 set sum [expr sqrt($sum)]
 set retval {}
 foreach term $v {
         lappend retval [expr $term / $sum]
                 }
 return $retval
}

}

minimize            500
run                 5000