set MOL pope-water set temp 500 set xbox 70 set ybox 70 set zbox 94 structure ${MOL}.psf coordinates ${MOL}.pdb temperature 0 parameters par_all27_prot_lipid.prm paraTypeCharmm on outputEnergies 100 outputTiming 100 xstFreq 100 dcdFreq 500 wrapAll on timestep 1 nonBondedFreq 2 fullElectFrequency 4 stepsPerCycle 20 exclude scaled1-4 1-4scaling 1.0 switching on switchDist 14 cutoff 16 pairlistdist 16 cellBasisVector1 $xbox 00.00 00.00 cellBasisVector2 00.00 $ybox 00.00 cellBasisVector3 00.00 00.00 $zbox cellOrigin -0.58 -0.78 0.056 Pme on PmeGridsizeX 60 PmeGridsizeY 60 PmeGridsizeZ 96 ######################################### # CONSTRAINTS ######################################### constraints on consRef ${MOL}-cons.pdb consKFile ${MOL}-cons.pdb consKCol B ######################################### # PRESSURE AND TEMPERATURE CONTRON ######################################### langevin on langevinDamping 5 langevinTemp $temp langevinHydrogen no useflexiblecell yes langevinPiston on langevinPistonTarget 1.01325 langevinPistonPeriod 100 langevinPistonDecay 50 langevinPistonTemp $temp binaryoutput off outputname ${MOL}-equil # GET INIT. ENERGY minimize 0 ########### # MINIMIZE ########### minimize 10000 output ${mol}-cons ####### # HEAT ####### set tem 1 while { $tem <= 500 } { langevinTemp $tem run 3000 set tem [expr $tem + 3] }