# configuration file to minimize, heat, equilibrate and alchemically mutate the protein structure

structure       /usergroup08/IA64/myrinet/jneelankatan/autumn07/NAMD/colicin/struct/1prw_solv.psf
coordinates     /usergroup08/IA64/myrinet/jneelankatan/autumn07/NAMD/colicin/struct/1prw_solv.pdb
bincoordinates  /usergroup08/IA64/myrinet/jneelankatan/autumn07/NAMD/colicin/struct/1prw_solv.coor

set output      prwsolv_min+heat+eq+FEP_run1

#
cellBasisVector1        74.508    0.0      0.0
cellBasisVector2         0.00    78.016    0.0
cellBasisVector3         0.00     0.00    172.903
cellOrigin               0.605   -0.769   0.056


# forcefield information

paratypecharmm          on
parameters              /usergroup08/IA64/myrinet/jneelankatan/autumn07/NAMD/CHARMMPARAMS.prm
exclude                 scaled1-4
1-4scaling              1.0
rigidBonds              water
wrapWater               on
wrapAll                 on



#
switching               on
switchdist              10.0
cutoff                  12.0
pairlistdist            13.5
#margin                   2.5
stepspercycle           20
nonbondedFreq           1
timestep                2.0  ;# 2fs/step

#
PME                     on
PMEGridSizeX            75
PMEGridSizeY            75
PMEGridSizeZ            180
fullElectFrequency      4




outputname              $output


restartfreq             500
dcdfreq                 100
xstFreq                 100
outputEnergies          500
outputPressure          500

set temperature         50
temperature             $temperature
set dstep               50


useGroupPressure        yes

langevin                on
langevinDamping         1.0
langevinHydrogen        off


BerendsenPressure                   on
BerendsenPressureTarget             1.01325
BerendsenPressureCompressibility    4.57E-5
BerendsenPressureRelaxationTime     100
BerendsenPressureFreq               4


minimize              20000
firsttimestep           0



# script for heating the system up to desired temperature

while { $temperature < 301 } {
        langevinTemp  $temperature
        if {$temperature == 300} {
            firsttimestep 0
            run 200000
        } else  {
            run 40000
        }
        set temperature [expr $temperature + $dstep]
}



# FEP PARAMETERS
source fep.tcl
fep on
fepFile 1prw_solv.fep
fepCol B
fepOutFile prwsolv_min+heat+eq+FEP_run1.fepout
fepOutFreq 10
fepEquilSteps 200000
set nSteps 2000000
set dLambda 0.1
set init { 0.02 0.1 }
set end { 0.9 0.98 }
runFEPlist $init $nSteps
runFEP 0.1 0.9 $dLambda $nSteps
runFEPlist $end $nSteps