set sys mos2_2.6+dna_grad numsteps 5000 structure ${sys}_ions.psf coordinates ${sys}_ions.pdb outputName ${sys}_min minimization on # system dimensions cellBasisVector1 88.19 0.0 0.0 cellBasisVector2 0.0 89.98 0.0 cellBasisVector3 0.0 0.0 219.98 cellOrigin 0.0 0.0 0.0 # parameters parameters ../c32b1/toppar/par_all27_na.prm parameters ../c32b1/toppar/par_all27_prot_lipid.prm parameters ./par_lj_MoS2.inp paraTypeCharmm on exclude scaled1-4 1-4scaling 1.0 switching on switchDist 10 cutoff 12 pairListDist 14 # integraion rigidBonds all timestep 2 nonBondedFreq 1 fullElectFrequency 2 stepsPerCycle 10 # output binaryOutput yes binaryRestart yes #wrapAll yes wrapNearest yes comMotion yes outputEnergies 1000 outputPressure 1000 outputTiming 1000 xstFreq 1000 dcdFreq 1000 restartFreq 1000 # electrostatics pme on pmeGridSizeX 96 pmeGridSizeY 96 pmeGridSizeZ 240 # external forces constraints on consKCol B consRef ${sys}_restrain.pdb consKFile ${sys}_restrain.pdb fixedAtoms on fixedAtomsFile ${sys}_fixed.pdb fixedAtomsCol B