methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/confout.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/gmx3_s.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/grompp.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/mdrun.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/start/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/start/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/start/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/start/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/start/gmx3_s.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/start/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/start/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/state.cpt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/state_prev.cpt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/#energy.xvg.1# methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/#mdrun.log.1# methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/2-MeSPH1.o1033877 methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/Forces-MethanolSPH-2-site.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/Potential-MethanolSPH-2-site.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/SPH-CGM-f-only.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/force.CGC-CGC.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/force.CGC-CGO.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/force.CGO-CGO.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/force.SPH-CGC.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/force.SPH-CGO.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/potential.CGC-CGC.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/potential.CGC-CGO.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/potential.CGO-CGO.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/potential.SPH-CGC.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/CGFF-figures/potential.SPH-CGO.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/RDFs.MethanolSPH.2-site.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/SPH-CGM-rdfs.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/bonds/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/bonds/BondDist.2-site.MethanolSPH.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/bonds/MethanolSPH.bond.dist.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/bonds/MethanolSPH.bond.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/bonds/MethanolSPH.bond.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/bonds/bond-dist.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/bonds/index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/calc_rdf.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/cgMethanolSPH.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/log.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/angle_O.CG.0.0-0.2.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/angle_O.CG.0.2-0.4.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/angle_O.CG.0.4-0.6.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/angle_O.CG.0.6-0.8.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/angle_O.CG.0.8-1.0.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/angle_O.CG.1.0-1.2.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/angle_O.CG.1.2-1.4.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/angle_O.CG.1.4-1.6.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/angle_O.CG.1.6-1.8.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/angle_O.CG.1.8-2.0.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/clean.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/do_calc.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/log.CG.0.0-0.2.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/log.CG.0.2-0.4.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/log.CG.0.4-0.6.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/log.CG.0.6-0.8.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/log.CG.0.8-1.0.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/log.CG.1.0-1.2.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/log.CG.1.2-1.4.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/log.CG.1.4-1.6.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/log.CG.1.6-1.8.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/log.CG.1.8-2.0.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/orient.CG.0.0-0.2.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/orient.CG.0.2-0.4.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/orient.CG.0.4-0.6.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/orient.CG.0.6-0.8.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/orient.CG.0.8-1.0.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/orient.CG.1.0-1.2.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/orient.CG.1.2-1.4.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/orient.CG.1.4-1.6.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/orient.CG.1.6-1.8.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/orient.CG.1.8-2.0.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGC.CG.0.0-0.2.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGC.CG.0.2-0.4.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGC.CG.0.4-0.6.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGC.CG.0.6-0.8.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGC.CG.0.8-1.0.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGC.CG.1.0-1.2.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGC.CG.1.2-1.4.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGC.CG.1.4-1.6.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGC.CG.1.6-1.8.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGC.CG.1.8-2.0.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGO.CG.0.0-0.2.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGO.CG.0.2-0.4.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGO.CG.0.4-0.6.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGO.CG.0.6-0.8.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGO.CG.0.8-1.0.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGO.CG.1.0-1.2.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGO.CG.1.2-1.4.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGO.CG.1.4-1.6.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGO.CG.1.6-1.8.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/rdf-SPH-CGO.CG.1.8-2.0.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/orientation/run.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/rdf.cg-sim.CGC-CGC.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/rdf.cg-sim.CGC-CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/rdf.cg-sim.CGC-CGO.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/rdf.cg-sim.CGC-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/rdf.cg-sim.CGO-CGO.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/rdf.cg-sim.CGO-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/rdf.cg-sim.SPH-CGC.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/rdf.cg-sim.SPH-CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/rdf.cg-sim.SPH-CGO.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/rdf.cg-sim.SPH-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/analysis/run.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/cgMethanolSPH.edr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/cgMethanolSPH.prod.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/confout.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/energy.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/grompp.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/mdrun.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/pressure.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/start/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/state.cpt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/state_prev.cpt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/#mdrun.log.1# methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/2-MeSPH2.o1033878 methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/cgMethanolSPH.edr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/cgMethanolSPH.prod.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/energy.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/grompp.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/mdrun.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/start/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/state.cpt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/state_prev.cpt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH2/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/Orientation-MethanolSPH.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/Orientation-MethanolSPH2.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/#mdrun.log.1# methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/CGFF-figures/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/CGFF-figures/force.SPH-CGC.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/CGFF-figures/force.SPH-CGO.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/CGFF-figures/potential.SPH-CGC.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/CGFF-figures/potential.SPH-CGO.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/MethanolSPH.prod.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/RDFs-MethanolSPH-2-site-fit-expans.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/bonds/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/bonds/BondDist-2-site-MethanolSPH-fit-expans.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/bonds/MethanolSPH.bond.dist.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/bonds/MethanolSPH.bond.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/bonds/MethanolSPH.bond.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/bonds/bond-dist.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/bonds/index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/calc_rdf.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/cgMethanolSPH.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/log.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/orientation.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/rdf.cg-sim.CGC-CGC.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/rdf.cg-sim.CGC-CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/rdf.cg-sim.CGC-CGO.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/rdf.cg-sim.CGC-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/rdf.cg-sim.CGO-CGO.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/rdf.cg-sim.CGO-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/rdf.cg-sim.SPH-CGC.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/rdf.cg-sim.SPH-CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/rdf.cg-sim.SPH-CGO.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/rdf.cg-sim.SPH-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/analysis/run.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/cgMethanolSPH.edr methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/cgMethanolSPH.prod.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/confout.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/fit.o1033885 methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/grompp.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/mdrun.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/state.cpt methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/state_prev.cpt methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/fit-MethanolSPH/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/#mdrun.log.1# methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/MethanolSPH.prod.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/RDFs-MethanolSPH-2-site-repulsive1-expans.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/bonds/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/bonds/BondDist-2-site-MethanolSPH-repulsive1.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/bonds/MethanolSPH.bond.dist.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/bonds/MethanolSPH.bond.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/bonds/MethanolSPH.bond.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/bonds/bond-dist.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/bonds/index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/calc_rdf.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/cgMethanolSPH.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/log.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/orientation.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/rdf.cg-sim.CGC-CGC.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/rdf.cg-sim.CGC-CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/rdf.cg-sim.CGC-CGO.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/rdf.cg-sim.CGC-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/rdf.cg-sim.CGO-CGO.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/rdf.cg-sim.CGO-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/rdf.cg-sim.SPH-CGC.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/rdf.cg-sim.SPH-CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/rdf.cg-sim.SPH-CGO.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/rdf.cg-sim.SPH-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/analysis/run.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/cgMethanolSPH.edr methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/cgMethanolSPH.prod.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/confout.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/grompp.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/mdrun.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/repulse1.o1033896 methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/run.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/start/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/state.cpt methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/state_prev.cpt methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive1/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/#mdrun.log.1# methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/RDFs-MethanolSPH-2-site-repulsive2-expans.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/bonds/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/bonds/BondDist-2-site-MethanolSPH2-repulsive2.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/bonds/MethanolSPH.bond.dist.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/bonds/MethanolSPH.bond.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/bonds/MethanolSPH.bond.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/bonds/bond-dist.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/bonds/index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/calc_rdf.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/cgMethanolSPH.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/repulsive2/analysis/cgMethanolSPH.tpr