methanol-ref/Mar17.2010/AA-traj-1000frames-Methanol/Methanol.ref.trr methanol-ref/Mar17.2010/AA-traj-1000frames-Methanol/reduce_frames.sh methanol-ref/PICTURES/ methanol-ref/PICTURES/mapping/ methanol-ref/PICTURES/mapping/aaFRAME.gro methanol-ref/PICTURES/mapping/aaMethanol-1Molec.jpg methanol-ref/PICTURES/mapping/aaMethanol-1Molec.tga methanol-ref/PICTURES/mapping/aaMethanolSPH.jpg methanol-ref/PICTURES/mapping/aaMethanolSPH.tga methanol-ref/PICTURES/mapping/cgFRAME.1site.gro methanol-ref/PICTURES/mapping/cgFRAME.2site.gro methanol-ref/PICTURES/mapping/cgMethanol-1Molec-1Site.jpg methanol-ref/PICTURES/mapping/cgMethanol-1Molec-1Site.tga methanol-ref/PICTURES/mapping/cgMethanol-1Molec-2Site.jpg methanol-ref/PICTURES/mapping/cgMethanol-1Molec-2Site.tga methanol-ref/PICTURES/mapping/cgMethanolSPH-1Site-mixed.jpg methanol-ref/PICTURES/mapping/cgMethanolSPH-1Site-mixed.tga methanol-ref/PICTURES/mapping/cgMethanolSPH-1Site.jpg methanol-ref/PICTURES/mapping/cgMethanolSPH-1Site.tga methanol-ref/PICTURES/mapping/cgMethanolSPH-2Site-mixed.jpg methanol-ref/PICTURES/mapping/cgMethanolSPH-2Site-mixed.tga methanol-ref/PICTURES/mapping/cgMethanolSPH-2Site.jpg methanol-ref/PICTURES/mapping/cgMethanolSPH-2Site.tga methanol-ref/PICTURES/mapping/mapping1.vmd methanol-ref/PICTURES/mapping/mapping2.vmd methanol-ref/PICTURES/mapping/mapping3.vmd methanol-ref/PICTURES/mapping/mapping4.vmd methanol-ref/PICTURES/mapping/mapping5.vmd methanol-ref/PICTURES/mapping/mapping6.vmd methanol-ref/PICTURES/mapping/new.jpg methanol-ref/PICTURES/mapping/new.tga methanol-ref/PICTURES/mapping/orientation.jpg methanol-ref/PICTURES/mapping/orientation.tga methanol-ref/PICTURES/mapping/state.may.14.2010 methanol-ref/PICTURES/mapping/state.may14.2010.vmd methanol-ref/RESULTS/ methanol-ref/RESULTS/Week.April.30.2010/ methanol-ref/RESULTS/Week.April.30.2010/AA/ methanol-ref/RESULTS/Week.April.30.2010/AA/orient.AA.0.0-0.2.dat methanol-ref/RESULTS/Week.April.30.2010/AA/orient.AA.0.2-0.4.dat methanol-ref/RESULTS/Week.April.30.2010/AA/orient.AA.0.4-0.6.dat methanol-ref/RESULTS/Week.April.30.2010/AA/orient.AA.0.6-0.8.dat methanol-ref/RESULTS/Week.April.30.2010/AA/orient.AA.0.8-1.0.dat methanol-ref/RESULTS/Week.April.30.2010/AA/orient.AA.1.0-1.2.dat methanol-ref/RESULTS/Week.April.30.2010/AA/orient.AA.1.2-1.4.dat methanol-ref/RESULTS/Week.April.30.2010/AA/orient.AA.1.4-1.6.dat methanol-ref/RESULTS/Week.April.30.2010/AA/orient.AA.1.6-1.8.dat methanol-ref/RESULTS/Week.April.30.2010/AA/orient.AA.1.8-2.0.dat methanol-ref/RESULTS/Week.April.30.2010/CG/ methanol-ref/RESULTS/Week.April.30.2010/CG/orient.CG.0.0-0.2.dat methanol-ref/RESULTS/Week.April.30.2010/CG/orient.CG.0.2-0.4.dat methanol-ref/RESULTS/Week.April.30.2010/CG/orient.CG.0.4-0.6.dat methanol-ref/RESULTS/Week.April.30.2010/CG/orient.CG.0.6-0.8.dat methanol-ref/RESULTS/Week.April.30.2010/CG/orient.CG.0.8-1.0.dat methanol-ref/RESULTS/Week.April.30.2010/CG/orient.CG.1.0-1.2.dat methanol-ref/RESULTS/Week.April.30.2010/CG/orient.CG.1.2-1.4.dat methanol-ref/RESULTS/Week.April.30.2010/CG/orient.CG.1.4-1.6.dat methanol-ref/RESULTS/Week.April.30.2010/CG/orient.CG.1.6-1.8.dat methanol-ref/RESULTS/Week.April.30.2010/CG/orient.CG.1.8-2.0.dat methanol-ref/RESULTS/Week.April.30.2010/orientation-updated-MetholSPH.agr methanol-ref/RESULTS/Week.Mar14-20.2010/ methanol-ref/RESULTS/Week.Mar14-20.2010/aa-potential-WCA/ methanol-ref/RESULTS/Week.Mar14-20.2010/aa-potential-WCA/MethanolSPH/ methanol-ref/RESULTS/Week.Mar14-20.2010/aa-potential-WCA/MethanolSPH/potential_SPH_C.dat methanol-ref/RESULTS/Week.Mar14-20.2010/aa-potential-WCA/MethanolSPH/potential_SPH_HC.dat methanol-ref/RESULTS/Week.Mar14-20.2010/aa-potential-WCA/MethanolSPH/potential_SPH_O.dat methanol-ref/RESULTS/Week.Mar14-20.2010/aa-potential-WCA/MethanolSPH2/ methanol-ref/RESULTS/Week.Mar14-20.2010/aa-potential-WCA/MethanolSPH2/potential_SPH_C.dat methanol-ref/RESULTS/Week.Mar14-20.2010/aa-potential-WCA/MethanolSPH2/potential_SPH_HC.dat methanol-ref/RESULTS/Week.Mar14-20.2010/aa-potential-WCA/MethanolSPH2/potential_SPH_O.dat methanol-ref/RESULTS/Week.Mar14-20.2010/aa-potential-WCA/WCA-AA-Potential.agr methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/ methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/ methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/Forces-CGM-SPH-1SiteModel.agr methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/Forces-CGMethanol-1SiteModel.agr methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/Methanol/ methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/Methanol/CGM-CGM-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/MethanolSPH/ methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/MethanolSPH/CGM-CGM-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/MethanolSPH/SPH-CGM-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/MethanolSPH2/ methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/MethanolSPH2/CGM-CGM-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/1-site/MethanolSPH2/SPH-CGM-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/ methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/Forces-CGM-2Site-Model.agr methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/Forces-SPH-CGM-2Site-Model.agr methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/Methanol/ methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/Methanol/CGC-CGC-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/Methanol/CGC-CGO-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/Methanol/CGO-CGO-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH/ methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH/CGC-CGC-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH/CGC-CGO-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH/CGO-CGO-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH/SPH-CGC-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH/SPH-CGO-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH2/ methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH2/CGC-CGC-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH2/CGC-CGO-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH2/CGO-CGO-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH2/SPH-CGC-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/2-site/MethanolSPH2/SPH-CGO-NB_PairInter-f-total.forces.dat methanol-ref/RESULTS/Week.Mar14-20.2010/cgff-forces-no-ref-potential/ABOUT methanol-ref/RESULTS/Week.Mar14-20.2010/document/ methanol-ref/RESULTS/Week.Mar14-20.2010/document/AA-Sims.tex methanol-ref/RESULTS/Week.Mar14-20.2010/document/CG-Sims.tex methanol-ref/RESULTS/Week.Mar14-20.2010/document/CGFF.tex methanol-ref/RESULTS/Week.Mar14-20.2010/document/Figures.log methanol-ref/RESULTS/Week.Mar14-20.2010/document/Figures.tex methanol-ref/RESULTS/Week.Mar14-20.2010/document/Methanol-ref.aux methanol-ref/RESULTS/Week.Mar14-20.2010/document/Methanol-ref.log methanol-ref/RESULTS/Week.Mar14-20.2010/document/Methanol-ref.pdf methanol-ref/RESULTS/Week.Mar14-20.2010/document/Methanol-ref.tex methanol-ref/RESULTS/Week.Mar14-20.2010/document/figures/ methanol-ref/RESULTS/Week.Mar14-20.2010/document/figures/Forces-CGM-2Site-Model.jpg methanol-ref/RESULTS/Week.Mar14-20.2010/document/figures/Forces-CGM-SPH-1SiteModel.jpg methanol-ref/RESULTS/Week.Mar14-20.2010/document/figures/Forces-CGMethanol-1SiteModel.jpg methanol-ref/RESULTS/Week.Mar14-20.2010/document/figures/Forces-SPH-CGM-2Site-Model.jpg methanol-ref/RESULTS/Week.Mar14-20.2010/document/figures/WCA-AA-Potential.jpg methanol-ref/RESULTS/Week.Mar21.2010/ methanol-ref/RESULTS/Week.Mar21.2010/BondDist-2-site-MethanolSPH.agr methanol-ref/RESULTS/Week.Mar21.2010/CGFF-forces-1000frames-1Site-Methanol.agr methanol-ref/RESULTS/Week.Mar21.2010/Compare-RDF-SPH-CGM-2Site-MethanolSHP.agr methanol-ref/RESULTS/Week.Mar21.2010/Forces-MethanolSPH-2-site.agr methanol-ref/RESULTS/Week.Mar21.2010/Orientation-MethanolSPH.agr methanol-ref/RESULTS/Week.Mar21.2010/Potential-MethanolSPH-2-site.agr methanol-ref/RESULTS/Week.Mar21.2010/RDFs-MethanolSPH-1site.agr methanol-ref/RESULTS/Week.Mar21.2010/RDFs-MethanolSPH-2-site.agr methanol-ref/RESULTS/Week.Mar21.2010/forces-1Site-MethanolSPH.agr methanol-ref/RESULTS/Week.Mar21.2010/not-used/ methanol-ref/RESULTS/Week.Mar21.2010/not-used/BondDist-2-site-MethanolSPH-fit-expans.agr methanol-ref/RESULTS/Week.Mar21.2010/not-used/BondDist-2-site-MethanolSPH-repulsive1.agr methanol-ref/RESULTS/Week.Mar21.2010/not-used/BondDist-2-site-MethanolSPH2-repulsive2.agr methanol-ref/RESULTS/Week.Mar21.2010/not-used/Orientation-MethanolSPH2.agr methanol-ref/RESULTS/Week.Mar21.2010/not-used/RDFs-MethanolSPH-2-site-fit-expans.agr methanol-ref/RESULTS/Week.Mar21.2010/not-used/RDFs-MethanolSPH-2-site-repulsive1-expans.agr methanol-ref/RESULTS/Week.Mar21.2010/not-used/RDFs-MethanolSPH-2-site-repulsive2-expans.agr methanol-ref/RESULTS/Week.Mar21.2010/not-used/RDFs-MethanolSPH2-1site.agr methanol-ref/RESULTS/Week.Mar21.2010/potential-1Site-MethanolSPH.agr methanol-ref/RESULTS/Week.Mar30.2010/ methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/ methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/ methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.0.0-0.4.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.0.1-0.5.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.0.2-0.6.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.0.3-0.7.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.0.4-0.8.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.0.5-0.9.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.0.6-1.0.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.0.7-1.1.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.0.8-1.2.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.0.9-1.3.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.1.0-1.4.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.1.1-1.5.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.1.2-1.6.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.1.3-1.7.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.1.4-1.8.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.1.5-1.9.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/AA/aaMethanolSPH.orientation.1.6-2.0.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/ methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.0.0-0.4.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.0.1-0.5.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.0.2-0.6.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.0.3-0.7.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.0.4-0.8.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.0.5-0.9.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.0.6-1.0.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.0.7-1.1.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.0.8-1.2.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.0.9-1.3.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.1.0-1.4.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.1.1-1.5.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.1.2-1.6.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.1.3-1.7.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.1.4-1.8.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.1.5-1.9.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/CG/aaMethanolSPH.orientation.1.6-2.0.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.4/Compare.orientation.2siteModel.agr methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/ methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/ methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.0.0-0.5.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.0.1-0.6.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.0.2-0.7.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.0.3-0.8.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.0.4-0.9.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.0.5-1.0.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.0.6-1.1.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.0.7-1.2.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.0.8-1.3.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.0.9-1.4.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.1.0-1.5.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.1.1-1.6.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.1.2-1.7.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.1.3-1.8.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.1.4-1.9.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/AA/aaMethanolSPH.orientation.1.5-2.0.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/ methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.0.0-0.5.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.0.1-0.6.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.0.2-0.7.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.0.3-0.8.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.0.4-0.9.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.0.5-1.0.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.0.6-1.1.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.0.7-1.2.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.0.8-1.3.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.0.9-1.4.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.1.0-1.5.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.1.1-1.6.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.1.2-1.7.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.1.3-1.8.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.1.4-1.9.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/CG/aaMethanolSPH.orientation.1.5-2.0.dat methanol-ref/RESULTS/Week.Mar30.2010/orientation-bin0.5/Orientation.bin0.5.agr methanol-ref/RESULTS/Week.Mar6-13.2010/ methanol-ref/RESULTS/Week.Mar6-13.2010/BondDist.2-site.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/ methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/ methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/forces/ methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/forces/f-CGM_CGM.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/forces/f-CGM_SPH.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/forces/forces.1-site.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/forces/p-CGM_CGM.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/forces/p-CGM_SPH.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/forces/potential.1-site.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/rdfs/ methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/rdfs/rdf.cg-sim.CGM-CGM.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/rdfs/rdf.cg-sim.SPH-CGM.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/rdfs/rdf.mapped.CGM-CGM.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/1-site/rdfs/rdf.mapped.SPH-CGM.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/ methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/bonds/ methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/bonds/cg-sim.MethanolSPH.bond.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/bonds/mapped-MethanolSPH.bond.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/ methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/f-CGC_CGC.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/f-CGC_CGO.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/f-CGC_SPH.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/f-CGO_CGO.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/f-CGO_SPH.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/p-CGC_CGC.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/p-CGC_CGO.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/p-CGC_SPH.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/p-CGO_CGO.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/forces/p-CGO_SPH.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/orientation/ methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/orientation/aa-map.MethanolSPH.orientation.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/orientation/cg-sim.MethanolSPH.orientation.dat methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/orientation/orientation.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/ methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/rdf.cg-sim.CGC-CGC.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/rdf.cg-sim.CGC-CGO.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/rdf.cg-sim.CGO-CGO.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/rdf.cg-sim.SPH-CGC.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/rdf.cg-sim.SPH-CGO.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/rdf.mapped.CGC-CGC.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/rdf.mapped.CGC-CGO.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/rdf.mapped.CGO-CGO.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/rdf.mapped.SPH-CGC.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/MethanolSPH/2-site/rdfs/rdf.mapped.SPH-CGO.xvg methanol-ref/RESULTS/Week.Mar6-13.2010/RDFs.MethanolSPH.1site.agr methanol-ref/RESULTS/Week.Mar6-13.2010/RDFs.MethanolSPH.2-site.agr methanol-ref/RESULTS/Week.Mar6-13.2010/document/ methanol-ref/RESULTS/Week.Mar6-13.2010/document/Figures.aux methanol-ref/RESULTS/Week.Mar6-13.2010/document/Figures.tex methanol-ref/RESULTS/Week.Mar6-13.2010/document/MethanolSPH.aux methanol-ref/RESULTS/Week.Mar6-13.2010/document/MethanolSPH.log methanol-ref/RESULTS/Week.Mar6-13.2010/document/MethanolSPH.pdf methanol-ref/RESULTS/Week.Mar6-13.2010/document/MethanolSPH.tex methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/ methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/BondDist-2-site-MethanolSPH.jpg methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/RDFs-MethanolSPH-1site.jpg methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/RDFs-MethanolSPH-2-site.jpg methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/forces-1-site-MethanolSPH.jpg methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/forces-2-site-MethanolSPH.jpg methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/orientation-MethanolSPH.jpg methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/potential-1-site-MethanolSPH.jpg methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/potential-2-site-MethanolSPH.jpg methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/xmgrace-files/ methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/xmgrace-files/BondDist.2-site.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/xmgrace-files/RDFs.MethanolSPH.1site.agr methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/xmgrace-files/RDFs.MethanolSPH.2-site.agr methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/xmgrace-files/forces.1-site.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/xmgrace-files/forces.2-site.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/xmgrace-files/orientation-MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/xmgrace-files/potential.1-site.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/document/figures/xmgrace-files/potential.2-site.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/forces.2-site.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/orientation.MethanolSPH.agr methanol-ref/RESULTS/Week.Mar6-13.2010/potential.2-site.MethanolSPH.agr methanol-ref/start_configuration/ methanol-ref/start_configuration/mdMethanol.ref.1.gro methanol-ref/start_configuration/mdMethanolSPH.ref.1.gro methanol-ref/start_configuration/mdMethanolSPH2.ref.1.gro methanol-ref/table_files/ methanol-ref/table_files/ABOUT methanol-ref/table_files/WCA-table-files.2/ methanol-ref/table_files/WCA-table-files.2/src/ methanol-ref/table_files/WCA-table-files.2/src/WCA-table.c methanol-ref/table_files/WCA-table-files.2/src/a.out methanol-ref/table_files/WCA-table-files.2/src/comp.sh methanol-ref/table_files/WCA-table-files/ methanol-ref/table_files/WCA-table-files/MethanolSPH/ methanol-ref/table_files/WCA-table-files/MethanolSPH/potential_SPH_C.dat methanol-ref/table_files/WCA-table-files/MethanolSPH/potential_SPH_HC.dat methanol-ref/table_files/WCA-table-files/MethanolSPH/potential_SPH_O.dat methanol-ref/table_files/WCA-table-files/MethanolSPH/run-WCA.sh methanol-ref/table_files/WCA-table-files/MethanolSPH/table_SPH_opls_154.xvg methanol-ref/table_files/WCA-table-files/MethanolSPH/table_SPH_opls_156.xvg methanol-ref/table_files/WCA-table-files/MethanolSPH/table_SPH_opls_157.xvg methanol-ref/table_files/WCA-table-files/MethanolSPH2/ methanol-ref/table_files/WCA-table-files/MethanolSPH2/potential_SPH_C.dat methanol-ref/table_files/WCA-table-files/MethanolSPH2/potential_SPH_HC.dat methanol-ref/table_files/WCA-table-files/MethanolSPH2/potential_SPH_O.dat methanol-ref/table_files/WCA-table-files/MethanolSPH2/run-WCA.sh methanol-ref/table_files/WCA-table-files/MethanolSPH2/table_SPH_opls_154.xvg methanol-ref/table_files/WCA-table-files/MethanolSPH2/table_SPH_opls_156.xvg methanol-ref/table_files/WCA-table-files/MethanolSPH2/table_SPH_opls_157.xvg methanol-ref/table_files/WCA-table-files/src/ methanol-ref/table_files/WCA-table-files/src/WCA-table.c methanol-ref/table_files/WCA-table-files/src/a.out methanol-ref/table_files/WCA-table-files/src/comp.sh methanol-ref/table_files/table_6_12/ methanol-ref/table_files/table_6_12/src/ methanol-ref/table_files/table_6_12/src/a.out methanol-ref/table_files/table_6_12/src/comp.sh methanol-ref/table_files/table_6_12/src/table.c methanol-ref/table_files/table_6_12/src/table.xvg methanol-ref/table_files/table_6_12/table.xvg methanol-ref/table_files/table_6_12/tablep.xvg