structure ion-meth.psf coordinates ion-meth.pdb paraTypeCharmm on parameters opls.inp temperature 298 vdwGeometricSigma on exclude scaled1-4 1-4scaling 1.0 cutoff 12. switching on switchdist 10. pairlistdist 13.5 timestep 2.0 ;# 2fs/step rigidBonds all ;# needed for 2fs steps nonbondedFreq 1 fullElectFrequency 2 stepspercycle 10 langevin on ;# do langevin dynamics langevinDamping 5 ;# damping coefficient (gamma) of 5/ps langevinTemp 298 langevinHydrogen off ;# don't couple langevin bath to hydrogens cellBasisVector1 24.402 0. 0. cellBasisVector2 0. 24.402 0. cellBasisVector3 0. 0 24.402 cellOrigin 0. 0. 0. wrapAll on PME yes PMEGridSizeX 25 PMEGridSizeY 25 PMEGridSizeZ 25 # Constant Pressure Control (variable volume) useGroupPressure yes ;# needed for rigidBonds useFlexibleCell no useConstantArea no langevinPiston on langevinPistonTarget 1.01325 ;# in bar -> 1 atm langevinPistonPeriod 100. langevinPistonDecay 50. langevinPistonTemp $temperature outputName ion-meth_fep restartfreq 500 ;# 500steps = every 1ps dcdfreq 100 xstFreq 250 outputEnergies 100 outputPressure 100 #FEP fep on fepFile ion-meth.fep fepCol B fepOutFile ion-meth.fepout fepOutFreq 5 FepEquilSteps 5000 set step 0.00 set dstep 0.025 while {$step < 1.00} { firsttimestep 0 lambda $step set step [expr $step+$dstep] lambda2 $step minimize 1000 run 10000 }