
amber on
parmfile dipeptide.top
ambercoor dipeptide.crd

temperature 300

exclude scaled1-4
1-4scaling 0.8333333

#timestep 2.0
#rigidBonds all
#fullElectFrequency 2

switching on
switchDist 9
cutoff  10
pairListDist 11

outputname output
outputEnergies 1
outputTiming   100
dcdFreq        500
restartFreq    500
wrapWater     on
wrapNearest   on

langevin          on
langevinDamping   2
langevinHydrogen  no
langevinTemp     300

apbsForces       on
apbsPQRFile      dipeptide.pqr
apbsForcesConfig {
#  dime 33 33 33
#  cglen    17.0 13.87 12.3
#  fglen    17.0 13.87 12.3

#  dime 0 0 0
  grid 1.01 1.0 1.0
 recalculateGrid on
  srfm 2
  chgm 1
  bcfl 1
  debug 0
  verbose 2
  pdie 2.0000
  sdie 78.5400
  sdens 10.00
  srad 1.40
  swin 0.30
  temp 298.15
  gamma 0.105
  sp_apbs on
  wpot on
}

#stepsPerCycle 1
#run 5

minimize 0
#numsteps 1000
#run 0
