# molecular system amber on parmfile clig.top ambercoor clig.crd firsttimestep 0 #temperature 0 set runnew min3 set runold min2 set temperature 300 bincoordinates ./${runold}-restart.coor binvelocities ./${runold}-restart.vel extendedSystem ./${runold}-restart.xsc # force field exclude scaled1-4 1-4scaling 0.833333 # nonbond interactions switching on switchdist 8.5 cutoff 10 pairlistdist 12 # integrator timestep 1 nonbondedFreq 2 FullElectFrequency 4 stepspercycle 20 #PME stuff #cellOrigin 64.48 61.11 80.69 #cellBasisVector1 125.00 000.00 000.00 #cellBasisVector2 000.00 119.00 000.00 #cellBasisVector3 000.00 000.00 158.00 PME on PmeGridsizeX 150 PmeGridsizeY 150 PmeGridsizeZ 160 # output outputname $runnew restartname ${runnew}-restart restartfreq 1000 dcdfreq 1000 outputEnergies 500 outputPressure 500 wrapall on wrapNearest on restartsave no #langevin on #langevinDamping 10 #langevinTemp 300 #langevinHydrogen on # #langevinPiston on #langevinPistonTarget 1.01325 #langevinPistonPeriod 200 #langevinPistonDecay 100 #langevinPistonTemp 300 # #useGroupPressure yes #useFlexibleCell no #useConstantRatio no extraBonds yes extraBondsFile 1_eb.txt # minimize fixed protein minimize 10000