methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/MethanolSPH2.ref.trr methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/confout.gro methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/grompp.log methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/mdout-MethanolSPH2.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/mdrun.log methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/mdrun0.log methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/mdrun1.log methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/mdrun2.log methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/mdrun3.log methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/mdrun4.log methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/mdrun5.log methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/mdrun6.log methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/mdrun7.log methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/methanol_oplsaa.itp methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/qsub.sh methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/run_gmx.sh methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/sphere.itp methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/ methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/MethanolSPH2.ref.gro methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/MethanolSPH2.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/MethanolSPH2.ref.top methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/methanol_oplsaa.itp methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/qsub.sh methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/run_gmx.sh methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/sphere.itp methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/table.xvg methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/table_SPH_opls_154.xvg methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/table_SPH_opls_156.xvg methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/table_SPH_opls_157.xvg methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/table_index.ndx methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/start/tablep.xvg methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/table.xvg methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/table_SPH_opls_154.xvg methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/table_SPH_opls_156.xvg methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/table_SPH_opls_157.xvg methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/table_index.ndx methanol-ref/AA-sims/TVN-DispCorrect/prod2-raw/MethanolSPH2/tablep.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/ methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/ methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/#Methanol.ref.edr.1# methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/#Methanol.ref.tpr.1# methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/#Methanol.ref.trr.1# methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/#mdout-Methanol.ref.mdp.1# methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/#mdrun0.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/#mdrun1.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/#mdrun2.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/#mdrun3.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/Methanol.o996446 methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/Methanol.o996573 methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/Methanol.ref.edr methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/Methanol.ref.gro methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/Methanol.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/Methanol.ref.top methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/Methanol.ref.tpr methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/Methanol.ref.trr methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/confout.gro methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/energy.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/grompp.log methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/mdout-Methanol.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/mdrun.log methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/mdrun0.log methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/mdrun1.log methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/mdrun2.log methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/mdrun3.log methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/methanol_oplsaa.itp methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/qsub.sh methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/run_gmx.sh methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/start/ methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/start/Methanol.ref.gro methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/start/Methanol.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/start/Methanol.ref.top methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/start/methanol_oplsaa.itp methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/start/qsub.sh methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/start/run_gmx.sh methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/start/table.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/start/tablep.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/table.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/Methanol/tablep.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/ methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/#MethanolSPH.ref.edr.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/#MethanolSPH.ref.tpr.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/#MethanolSPH.ref.trr.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/#mdout-MethanolSPH.ref.mdp.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/#mdrun0.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/#mdrun1.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/#mdrun2.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/#mdrun3.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/MethanolSPH.o996567 methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/MethanolSPH.o996574 methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/MethanolSPH.ref.edr methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/MethanolSPH.ref.gro methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/MethanolSPH.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/MethanolSPH.ref.top methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/MethanolSPH.ref.tpr methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/MethanolSPH.ref.trr methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/confout.gro methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/energy.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/grompp.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/mdout-MethanolSPH.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/mdrun.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/mdrun0.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/mdrun1.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/mdrun2.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/mdrun3.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/methanol_oplsaa.itp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/qsub.sh methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/run_gmx.sh methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/sphere.itp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/ methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/MethanolSPH.ref.gro methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/MethanolSPH.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/MethanolSPH.ref.top methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/methanol_oplsaa.itp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/qsub.sh methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/run_gmx.sh methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/sphere.itp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/table.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/table_SPH_opls_154.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/table_SPH_opls_156.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/table_SPH_opls_157.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/table_index.ndx methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/start/tablep.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/table.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/table_SPH_opls_154.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/table_SPH_opls_156.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/table_SPH_opls_157.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/table_index.ndx methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH/tablep.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/ methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/#MethanolSPH2.ref.edr.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/#MethanolSPH2.ref.tpr.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/#MethanolSPH2.ref.trr.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/#mdout-MethanolSPH2.ref.mdp.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/#mdrun0.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/#mdrun1.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/#mdrun2.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/#mdrun3.log.1# methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/MethanolSPH2.o996568 methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/MethanolSPH2.o996575 methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/MethanolSPH2.ref.edr methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/MethanolSPH2.ref.gro methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/MethanolSPH2.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/MethanolSPH2.ref.top methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/MethanolSPH2.ref.tpr methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/MethanolSPH2.ref.trr methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/confout.gro methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/grompp.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/mdout-MethanolSPH2.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/mdrun.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/mdrun0.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/mdrun1.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/mdrun2.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/mdrun3.log methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/methanol_oplsaa.itp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/qsub.sh methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/run_gmx.sh methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/sphere.itp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/ methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/MethanolSPH2.ref.gro methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/MethanolSPH2.ref.mdp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/MethanolSPH2.ref.top methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/methanol_oplsaa.itp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/qsub.sh methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/run_gmx.sh methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/sphere.itp methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/table.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/table_SPH_opls_154.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/table_SPH_opls_156.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/table_SPH_opls_157.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/table_index.ndx methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/start/tablep.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/table.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/table_SPH_opls_154.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/table_SPH_opls_156.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/table_SPH_opls_157.xvg methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/table_index.ndx methanol-ref/AA-sims/TVN-DispCorrect/test/MethanolSPH2/tablep.xvg methanol-ref/CG-sims/ methanol-ref/CG-sims/using-forces/ methanol-ref/CG-sims/using-forces/1-site/ methanol-ref/CG-sims/using-forces/1-site/prod/ methanol-ref/CG-sims/using-forces/1-site/prod/MethanolSPH.prod.log methanol-ref/CG-sims/using-forces/1-site/prod/analysis/ methanol-ref/CG-sims/using-forces/1-site/prod/analysis/calc_rdf.sh methanol-ref/CG-sims/using-forces/1-site/prod/analysis/cgMethanolSPH.gro methanol-ref/CG-sims/using-forces/1-site/prod/analysis/cgMethanolSPH.ndx methanol-ref/CG-sims/using-forces/1-site/prod/analysis/cgMethanolSPH.tpr methanol-ref/CG-sims/using-forces/1-site/prod/analysis/cgMethanolSPH.trr methanol-ref/CG-sims/using-forces/1-site/prod/analysis/rdf.cg-sim.CGM-CGM.log methanol-ref/CG-sims/using-forces/1-site/prod/analysis/rdf.cg-sim.CGM-CGM.xvg methanol-ref/CG-sims/using-forces/1-site/prod/analysis/rdf.cg-sim.SPH-CGM.log methanol-ref/CG-sims/using-forces/1-site/prod/analysis/rdf.cg-sim.SPH-CGM.xvg methanol-ref/CG-sims/using-forces/1-site/prod/cg-1site.o1019260 methanol-ref/CG-sims/using-forces/1-site/prod/cgMethanolSPH.edr methanol-ref/CG-sims/using-forces/1-site/prod/cgMethanolSPH.gro methanol-ref/CG-sims/using-forces/1-site/prod/cgMethanolSPH.mdp methanol-ref/CG-sims/using-forces/1-site/prod/cgMethanolSPH.top methanol-ref/CG-sims/using-forces/1-site/prod/cgMethanolSPH.tpr methanol-ref/CG-sims/using-forces/1-site/prod/cgMethanolSPH.trr methanol-ref/CG-sims/using-forces/1-site/prod/confout.gro methanol-ref/CG-sims/using-forces/1-site/prod/energy.xvg methanol-ref/CG-sims/using-forces/1-site/prod/grompp.log methanol-ref/CG-sims/using-forces/1-site/prod/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-forces/1-site/prod/mdrun.log methanol-ref/CG-sims/using-forces/1-site/prod/mdrun0.log methanol-ref/CG-sims/using-forces/1-site/prod/mdrun1.log methanol-ref/CG-sims/using-forces/1-site/prod/mdrun2.log methanol-ref/CG-sims/using-forces/1-site/prod/mdrun3.log methanol-ref/CG-sims/using-forces/1-site/prod/mdrun4.log methanol-ref/CG-sims/using-forces/1-site/prod/mdrun5.log methanol-ref/CG-sims/using-forces/1-site/prod/mdrun6.log methanol-ref/CG-sims/using-forces/1-site/prod/mdrun7.log methanol-ref/CG-sims/using-forces/1-site/prod/qsub.sh methanol-ref/CG-sims/using-forces/1-site/prod/reduce_frames.sh methanol-ref/CG-sims/using-forces/1-site/prod/run_gmx.sh methanol-ref/CG-sims/using-forces/1-site/prod/table.xvg methanol-ref/CG-sims/using-forces/1-site/prod/table_CGM_CGM.xvg methanol-ref/CG-sims/using-forces/1-site/prod/table_CGM_SPH.xvg methanol-ref/CG-sims/using-forces/1-site/prod/table_index.ndx methanol-ref/CG-sims/using-forces/1-site/short-test/ methanol-ref/CG-sims/using-forces/1-site/short-test/MethanolSPH.o1019258 methanol-ref/CG-sims/using-forces/1-site/short-test/cgMethanolSPH.edr methanol-ref/CG-sims/using-forces/1-site/short-test/cgMethanolSPH.gro methanol-ref/CG-sims/using-forces/1-site/short-test/cgMethanolSPH.mdp methanol-ref/CG-sims/using-forces/1-site/short-test/cgMethanolSPH.top methanol-ref/CG-sims/using-forces/1-site/short-test/cgMethanolSPH.tpr methanol-ref/CG-sims/using-forces/1-site/short-test/cgMethanolSPH.trr methanol-ref/CG-sims/using-forces/1-site/short-test/confout.gro methanol-ref/CG-sims/using-forces/1-site/short-test/grompp.log methanol-ref/CG-sims/using-forces/1-site/short-test/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-forces/1-site/short-test/mdrun.log methanol-ref/CG-sims/using-forces/1-site/short-test/mdrun0.log methanol-ref/CG-sims/using-forces/1-site/short-test/mdrun1.log methanol-ref/CG-sims/using-forces/1-site/short-test/mdrun2.log methanol-ref/CG-sims/using-forces/1-site/short-test/mdrun3.log methanol-ref/CG-sims/using-forces/1-site/short-test/qsub.sh methanol-ref/CG-sims/using-forces/1-site/short-test/run_gmx.sh methanol-ref/CG-sims/using-forces/1-site/short-test/start/ methanol-ref/CG-sims/using-forces/1-site/short-test/start/cgMethanolSPH.gro methanol-ref/CG-sims/using-forces/1-site/short-test/start/cgMethanolSPH.mdp methanol-ref/CG-sims/using-forces/1-site/short-test/start/cgMethanolSPH.top methanol-ref/CG-sims/using-forces/1-site/short-test/start/gmx3_s.sh methanol-ref/CG-sims/using-forces/1-site/short-test/start/table.xvg methanol-ref/CG-sims/using-forces/1-site/short-test/start/table_CGM_CGM.xvg methanol-ref/CG-sims/using-forces/1-site/short-test/start/table_CGM_SPH.xvg methanol-ref/CG-sims/using-forces/1-site/short-test/start/table_index.ndx methanol-ref/CG-sims/using-forces/1-site/short-test/table.xvg methanol-ref/CG-sims/using-forces/1-site/short-test/table_CGM_CGM.xvg methanol-ref/CG-sims/using-forces/1-site/short-test/table_CGM_SPH.xvg methanol-ref/CG-sims/using-forces/1-site/short-test/table_index.ndx methanol-ref/CG-sims/using-forces/1-site/short-test/traj.xtc methanol-ref/CG-sims/using-forces/2-site/ methanol-ref/CG-sims/using-forces/2-site/original/ methanol-ref/CG-sims/using-forces/2-site/original/CGC-CGC-f.ref.dat methanol-ref/CG-sims/using-forces/2-site/original/CGC-CGO-f.ref.dat methanol-ref/CG-sims/using-forces/2-site/original/CGO-CGO-f.ref.dat methanol-ref/CG-sims/using-forces/2-site/original/SPH-CGC-NB_PairInter-f-total.forces.dat methanol-ref/CG-sims/using-forces/2-site/original/SPH-CGO-NB_PairInter-f-total.forces.dat methanol-ref/CG-sims/using-forces/2-site/prod/ methanol-ref/CG-sims/using-forces/2-site/prod/MethanolSPH.o1019245 methanol-ref/CG-sims/using-forces/2-site/prod/MethanolSPH.prod.log methanol-ref/CG-sims/using-forces/2-site/prod/analysis/ methanol-ref/CG-sims/using-forces/2-site/prod/analysis/bonds/ methanol-ref/CG-sims/using-forces/2-site/prod/analysis/bonds/MethanolSPH.bond.dist.xvg methanol-ref/CG-sims/using-forces/2-site/prod/analysis/bonds/MethanolSPH.bond.log methanol-ref/CG-sims/using-forces/2-site/prod/analysis/bonds/MethanolSPH.bond.xvg methanol-ref/CG-sims/using-forces/2-site/prod/analysis/bonds/bond-dist.sh methanol-ref/CG-sims/using-forces/2-site/prod/analysis/bonds/index.ndx methanol-ref/CG-sims/using-forces/2-site/prod/analysis/calc_rdf.sh methanol-ref/CG-sims/using-forces/2-site/prod/analysis/cgMethanolSPH.gro methanol-ref/CG-sims/using-forces/2-site/prod/analysis/cgMethanolSPH.ndx methanol-ref/CG-sims/using-forces/2-site/prod/analysis/cgMethanolSPH.tpr methanol-ref/CG-sims/using-forces/2-site/prod/analysis/cgMethanolSPH.trr methanol-ref/CG-sims/using-forces/2-site/prod/analysis/orientation/ methanol-ref/CG-sims/using-forces/2-site/prod/analysis/orientation/cg-sim.MethanolSPH.orientation.dat methanol-ref/CG-sims/using-forces/2-site/prod/analysis/orientation/log.txt methanol-ref/CG-sims/using-forces/2-site/prod/analysis/orientation/run.sh methanol-ref/CG-sims/using-forces/2-site/prod/analysis/rdf.cg-sim.CGC-CGC.log methanol-ref/CG-sims/using-forces/2-site/prod/analysis/rdf.cg-sim.CGC-CGC.xvg methanol-ref/CG-sims/using-forces/2-site/prod/analysis/rdf.cg-sim.CGC-CGO.log methanol-ref/CG-sims/using-forces/2-site/prod/analysis/rdf.cg-sim.CGC-CGO.xvg methanol-ref/CG-sims/using-forces/2-site/prod/analysis/rdf.cg-sim.CGO-CGO.log methanol-ref/CG-sims/using-forces/2-site/prod/analysis/rdf.cg-sim.CGO-CGO.xvg methanol-ref/CG-sims/using-forces/2-site/prod/analysis/rdf.cg-sim.SPH-CGC.log methanol-ref/CG-sims/using-forces/2-site/prod/analysis/rdf.cg-sim.SPH-CGC.xvg methanol-ref/CG-sims/using-forces/2-site/prod/analysis/rdf.cg-sim.SPH-CGO.log methanol-ref/CG-sims/using-forces/2-site/prod/analysis/rdf.cg-sim.SPH-CGO.xvg methanol-ref/CG-sims/using-forces/2-site/prod/cgMethanolSPH.edr methanol-ref/CG-sims/using-forces/2-site/prod/cgMethanolSPH.gro methanol-ref/CG-sims/using-forces/2-site/prod/cgMethanolSPH.mdp methanol-ref/CG-sims/using-forces/2-site/prod/cgMethanolSPH.top methanol-ref/CG-sims/using-forces/2-site/prod/cgMethanolSPH.tpr methanol-ref/CG-sims/using-forces/2-site/prod/cgMethanolSPH.trr methanol-ref/CG-sims/using-forces/2-site/prod/confout.gro methanol-ref/CG-sims/using-forces/2-site/prod/energy.xvg methanol-ref/CG-sims/using-forces/2-site/prod/grompp.log methanol-ref/CG-sims/using-forces/2-site/prod/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-forces/2-site/prod/mdrun.log methanol-ref/CG-sims/using-forces/2-site/prod/mdrun0.log methanol-ref/CG-sims/using-forces/2-site/prod/mdrun1.log methanol-ref/CG-sims/using-forces/2-site/prod/mdrun2.log methanol-ref/CG-sims/using-forces/2-site/prod/mdrun3.log methanol-ref/CG-sims/using-forces/2-site/prod/mdrun4.log methanol-ref/CG-sims/using-forces/2-site/prod/mdrun5.log methanol-ref/CG-sims/using-forces/2-site/prod/mdrun6.log methanol-ref/CG-sims/using-forces/2-site/prod/mdrun7.log methanol-ref/CG-sims/using-forces/2-site/prod/qsub.sh methanol-ref/CG-sims/using-forces/2-site/prod/reduce_frames.sh methanol-ref/CG-sims/using-forces/2-site/prod/run_gmx.sh methanol-ref/CG-sims/using-forces/2-site/prod/table.xvg methanol-ref/CG-sims/using-forces/2-site/prod/table_CGC_CGC.xvg methanol-ref/CG-sims/using-forces/2-site/prod/table_CGC_CGO.xvg methanol-ref/CG-sims/using-forces/2-site/prod/table_CGC_SPH.xvg methanol-ref/CG-sims/using-forces/2-site/prod/table_CGO_CGO.xvg methanol-ref/CG-sims/using-forces/2-site/prod/table_CGO_SPH.xvg methanol-ref/CG-sims/using-forces/2-site/prod/table_index.ndx methanol-ref/CG-sims/using-forces/2-site/tables/ methanol-ref/CG-sims/using-forces/2-site/tables/do_table.sh methanol-ref/CG-sims/using-forces/2-site/tables/f-CGC_CGC.dat methanol-ref/CG-sims/using-forces/2-site/tables/f-CGC_CGO.dat methanol-ref/CG-sims/using-forces/2-site/tables/f-CGC_SPH.dat methanol-ref/CG-sims/using-forces/2-site/tables/f-CGO_CGO.dat methanol-ref/CG-sims/using-forces/2-site/tables/f-CGO_SPH.dat methanol-ref/CG-sims/using-forces/2-site/tables/p-CGC_CGC.dat methanol-ref/CG-sims/using-forces/2-site/tables/p-CGC_CGO.dat methanol-ref/CG-sims/using-forces/2-site/tables/p-CGC_SPH.dat methanol-ref/CG-sims/using-forces/2-site/tables/p-CGO_CGO.dat methanol-ref/CG-sims/using-forces/2-site/tables/p-CGO_SPH.dat methanol-ref/CG-sims/using-forces/2-site/tables/run.sh methanol-ref/CG-sims/using-forces/2-site/tables/smooth-f.CGC-CGC.dat methanol-ref/CG-sims/using-forces/2-site/tables/smooth-f.CGC-CGO.dat methanol-ref/CG-sims/using-forces/2-site/tables/smooth-f.CGC-SPH.dat methanol-ref/CG-sims/using-forces/2-site/tables/smooth-f.CGO-CGO.dat methanol-ref/CG-sims/using-forces/2-site/tables/smooth-f.CGO-SPH.dat methanol-ref/CG-sims/using-forces/2-site/tables/table_CGC_CGC.xvg methanol-ref/CG-sims/using-forces/2-site/tables/table_CGC_CGO.xvg methanol-ref/CG-sims/using-forces/2-site/tables/table_CGC_SPH.xvg methanol-ref/CG-sims/using-forces/2-site/tables/table_CGO_CGO.xvg methanol-ref/CG-sims/using-forces/2-site/tables/table_CGO_SPH.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/ methanol-ref/CG-sims/using-forces/2-site/test-sim/MethanolSPH.o1019242 methanol-ref/CG-sims/using-forces/2-site/test-sim/cgMethanolSPH.edr methanol-ref/CG-sims/using-forces/2-site/test-sim/cgMethanolSPH.gro methanol-ref/CG-sims/using-forces/2-site/test-sim/cgMethanolSPH.mdp methanol-ref/CG-sims/using-forces/2-site/test-sim/cgMethanolSPH.top methanol-ref/CG-sims/using-forces/2-site/test-sim/cgMethanolSPH.tpr methanol-ref/CG-sims/using-forces/2-site/test-sim/cgMethanolSPH.trr methanol-ref/CG-sims/using-forces/2-site/test-sim/confout.gro methanol-ref/CG-sims/using-forces/2-site/test-sim/grompp.log methanol-ref/CG-sims/using-forces/2-site/test-sim/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-forces/2-site/test-sim/mdrun.log methanol-ref/CG-sims/using-forces/2-site/test-sim/mdrun0.log methanol-ref/CG-sims/using-forces/2-site/test-sim/mdrun1.log methanol-ref/CG-sims/using-forces/2-site/test-sim/mdrun2.log methanol-ref/CG-sims/using-forces/2-site/test-sim/mdrun3.log methanol-ref/CG-sims/using-forces/2-site/test-sim/qsub.sh methanol-ref/CG-sims/using-forces/2-site/test-sim/run_gmx.sh methanol-ref/CG-sims/using-forces/2-site/test-sim/start/ methanol-ref/CG-sims/using-forces/2-site/test-sim/start/cgMethanolSPH.gro methanol-ref/CG-sims/using-forces/2-site/test-sim/start/cgMethanolSPH.mdp methanol-ref/CG-sims/using-forces/2-site/test-sim/start/cgMethanolSPH.top methanol-ref/CG-sims/using-forces/2-site/test-sim/start/gmx3_s.sh methanol-ref/CG-sims/using-forces/2-site/test-sim/start/table.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/start/table_CGC_CGC.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/start/table_CGC_CGO.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/start/table_CGC_SPH.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/start/table_CGO_CGO.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/start/table_CGO_SPH.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/start/table_index.ndx methanol-ref/CG-sims/using-forces/2-site/test-sim/table.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/table_CGC_CGC.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/table_CGC_CGO.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/table_CGC_SPH.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/table_CGO_CGO.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/table_CGO_SPH.xvg methanol-ref/CG-sims/using-forces/2-site/test-sim/table_index.ndx methanol-ref/CG-sims/using-forces/2-site/test-sim/traj.xtc methanol-ref/CG-sims/using-structures/ methanol-ref/CG-sims/using-structures/preparing-files/ methanol-ref/CG-sims/using-structures/preparing-files/1-site/ methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/ methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/ methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/qsub.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/reduce_frames.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/run_gmx.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/table.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/table_CGM_CGM.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/table_CGM_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/start-files/table_index.ndx methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/tables/ methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/tables/CGM-CGM-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/tables/original-forces/ methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/tables/original-forces/CGM-CGM-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/tables/original-forces/SPH-CGM-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/tables/run.make_gmx4_table.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/tables/smooth-f.SPH-CGM.dat methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/tables/table_CGM_CGM.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH/tables/table_CGM_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/ methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/confout.gro methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/ener.edr methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/gmx4_s.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/md.log methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/mdout.mdp methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/qsub.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/reduce_frames.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/run_gmx.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/start-files/ methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/start-files/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/start-files/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/start-files/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/start-files/qsub.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/start-files/reduce_frames.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/start-files/table.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/start-files/table_CGM_CGM.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/start-files/table_CGM_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/start-files/table_index.ndx methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/state.cpt methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/table.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/table_CGM_CGM.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/table_CGM_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/table_index.ndx methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/tables/ methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/tables/CGM-CGM-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/tables/SPH-CGM-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/tables/original-forces/ methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/tables/original-forces/CGM-CGM-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/tables/original-forces/SPH-CGM-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/tables/run.make_gmx4_table.sh methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/tables/smooth-f.SPH-CGM.dat methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/tables/table_CGM_CGM.xvg methanol-ref/CG-sims/using-structures/preparing-files/1-site/MethanolSPH2/tables/table_CGM_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/qsub.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/reduce_frames.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/table.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/start-files/table_index.ndx methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/CGC-CGC-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/CGC-CGO-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/CGO-CGO-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/SPH-CGC-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/SPH-CGO-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/fit-expansion/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/fit-expansion/fit.SPH-CGC.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/fit-expansion/fit.SPH-CGO.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/fit-expansion/old.SPH-CGC.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/fit-expansion/old.SPH-CGO.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/fit-expansion/run.make_gmx4_table.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/fit-expansion/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/fit-expansion/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/original-forces/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/original-forces/CGC-CGC-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/original-forces/CGC-CGO-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/original-forces/CGO-CGO-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/original-forces/SPH-CGC-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/original-forces/SPH-CGO-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/original-forces/out.txt methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/out.txt methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/potent-12-inv-fit/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/potent-12-inv-fit/final.fit.SPH-CGC.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/potent-12-inv-fit/final.fit.SPH-CGO.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/potent-12-inv-fit/run.make_gmx4_table.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/potent-12-inv-fit/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/potent-12-inv-fit/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/run.make_gmx4_table.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/smooth-f.SPH-CGC.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/smooth-f.SPH-CGO.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/temp/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/temp/f-CGC-SPH.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/temp/f-CGO-SPH.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/temp/run.make_gmx4_table.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/temp/smooth-f.SPH-CGC.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/temp/smooth-f.SPH-CGO.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/temp/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH/tables/temp/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/ener.edr methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/gmx4_s.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/md.log methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/mdout.mdp methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/qsub.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/reduce_frames.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/run_gmx.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/qsub.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/reduce_frames.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/table.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/start_files/table_index.ndx methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/state.cpt methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/table.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/table_index.ndx methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/CGC-CGC-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/CGC-CGO-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/CGO-CGO-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/SPH-CGC-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/SPH-CGO-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/gmx4_s.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/original-forces/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/original-forces/CGC-CGC-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/original-forces/CGC-CGO-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/original-forces/CGO-CGO-f.ref.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/original-forces/SPH-CGC-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/original-forces/SPH-CGO-NB_PairInter-f-total.struct.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/original-forces/out.txt methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/out.txt methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/potent-12-inv-fit/ methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/potent-12-inv-fit/final-fit.SPH-CGC.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/potent-12-inv-fit/final-fit.SPH-CGO.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/potent-12-inv-fit/run.make_gmx4_table.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/potent-12-inv-fit/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/potent-12-inv-fit/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/run.make_gmx4_table.sh methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/smooth-f.SPH-CGC.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/smooth-f.SPH-CGO.dat methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/table.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/table_CGC_CGC.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/table_CGC_CGO.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/table_CGC_SPH.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/table_CGO_CGO.xvg methanol-ref/CG-sims/using-structures/preparing-files/2-site/MethanolSPH2/tables/table_CGO_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/ methanol-ref/CG-sims/using-structures/prod-sims/1-site/ methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/ methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/#mdrun.log.1# methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/1-MeSPH1.o1033868 methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/ methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/RDFs.MethanolSPH.1site.agr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/calc_rdf.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/cgMethanolSPH.ndx methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/rdf.cg-sim.CGM-CGM.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/rdf.cg-sim.CGM-CGM.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/rdf.cg-sim.SPH-CGM.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/analysis/rdf.cg-sim.SPH-CGM.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgMethanol.prod.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgMethanolSPH.edr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgMethanolSPH.prod.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgff-figures/ methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgff-figures/CGFF-Force-1Site-Methanol.agr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgff-figures/force.CGM-CGM.dat methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgff-figures/force.SPH-CGM.dat methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgff-figures/forces-1Site-MethanolSPH.agr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgff-figures/potential-1Site-MethanolSPH.agr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgff-figures/potential.CGM-CGM.dat methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/cgff-figures/potential.SPH-CGM.dat methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/confout.gro methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/grompp.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/mdrun.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/ methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/table_CGM_CGM.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/table_CGM_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/start/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/state.cpt methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/state_prev.cpt methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/table_CGM_CGM.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/table_CGM_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/ methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/#mdrun.log.1# methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/1-MeSPH2.o1033873 methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/ methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/RDFs.MethanolSPH2.1site.agr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/calc_rdf.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/cgMethanolSPH.ndx methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/rdf.cg-sim.CGM-CGM.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/rdf.cg-sim.CGM-CGM.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/rdf.cg-sim.SPH-CGM.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/analysis/rdf.cg-sim.SPH-CGM.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/cgMethanolSPH.edr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/cgMethanolSPH.prod.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/cgMethanolSPH2.prod.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/confout.gro methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/grompp.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/mdout-cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/mdrun.log methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/ methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/qsub.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/reduce_frames.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/run_gmx.sh methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/table_CGM_CGM.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/table_CGM_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/start/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/state.cpt methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/state_prev.cpt methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/table.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/table_CGM_CGM.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/table_CGM_SPH.xvg methanol-ref/CG-sims/using-structures/prod-sims/1-site/MethanolSPH2/table_index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/#mdrun.log.1# methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/2-MeSPH1.o1072010 methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.0.0-0.4.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.0.1-0.5.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.0.2-0.6.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.0.3-0.7.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.0.4-0.8.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.0.5-0.9.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.0.6-1.0.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.0.7-1.1.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.0.8-1.2.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.0.9-1.3.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.1.0-1.4.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.1.1-1.5.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.1.2-1.6.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.1.3-1.7.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.1.4-1.8.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.1.5-1.9.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/aaMethanolSPH.orientation.1.6-2.0.dat methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/cgMethanolSPH.tpr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/cgMethanolSPH.trr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/clean.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/do_calc.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/homodimer.orientation.agr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/log.txt methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/rdfs/ methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/rdfs/index.ndx methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/rdfs/rdf-CGC-CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/rdfs/rdf-CGC-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/rdfs/rdf-CGO-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/rdfs/rdf-SPH-CGC.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/rdfs/rdf-SPH-CGO.xvg methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/analysis/run.sh methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/cgMethanolSPH.edr methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/cgMethanolSPH.gro methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/cgMethanolSPH.mdp methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/cgMethanolSPH.prod.log methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/cgMethanolSPH.top methanol-ref/CG-sims/using-structures/prod-sims/2-site/MethanolSPH-dummy/cgMethanolSPH.tpr