cwd /iodisk1/home/wujh/md/heat # molecular system structure /iodisk1/home/wujh/md/ionized.psf coordinates /iodisk1/home/wujh/md/heat/miniout.coor # force field paratypecharmm on parameters /iodisk1/home/wujh/md/par_all27_prot_lipid.inp exclude scaled1-4 1-4scaling 1.0 # Restart Control firsttimestep 0 binaryoutput no restartname PSEres restartsave no restartfreq 1000 Binaryrestart yes # approximations switching on switchdist 8 cutoff 12 pairlistdist 15 stepspercycle 10 #integrator timestep 1.0 #output outputenergies 10 outputtiming 100 cellBasisVector1 79.672 0.0 0.0 cellBasisVector2 0.0 84.715 0.0 cellBasisVector3 0.0 0.0 161.068 cellOrigin -4.58 -8.01 75.00 wrapAll on wrapWater on PME yes PMEGridSizeX 80 PMEGridSizeY 90 PMEGridSizeZ 180 temperature 0 reassignFreq 200 reassignTemp 10 reassignIncr 10 reassignHold 298 #fixatoms fixedAtoms on fixedAtomsForces off fixedAtomsFile /iodisk1/home/wujh/md/heat/fixed.pdb fixedAtomsCol B #output outputname heatout #protocol DCDfile heatout.dcd dcdfreq 100 velDCDfile heatout.dcv velDCDfreq 100 XSTfile INTdcd.xst XSTfreq 100 run 20000