T20　is　the　first　fusion　inhibitor,　and　it　is　allowed　marketing　approval　from　the　FDA.　Nevertheless,　its　application　may　be　confined　because　of　the　high　cost,　virus　resistance　T20,　and　lack　of　oral　availability.　Therefore,　it　is　necessary　to　develop　more　potent　fusion　inhibitor,　and　for　this　purpose,　we　analyzed　the　interactions　between　gp41　and　T20.　In　that　article,　we　have　built　three-dimensional　model　of　the　two　peptide　(the　fusion　peptide　and　the　N-terminal　heptad　repeat　of　gp41,　and　T20)　using　the　modeling　and　molecular　dynamics　(MD)　simulation.　The　results　were　obtained　Procheck　program　displays　three-dimensional　model　were　sufficiently　accurate.　By　using　docking　and　MD　simulations,　we　verify　that　the　three　residues　from　the　segment　of　LLSGIV　in　NHR　of　gp41　have　large　binding　affinities　with　the　T20.　In　addition　we　also　verify　the　three　residues　from　the　lipid-binding　domain　of　T20　have　great　binding　free　energy　with　the　gp41.　We　wish　that　our　results　could　be　used　to　design　more　effective　HIV-1　fusion　inhibitors　targeted　to　HIV-1　gp41.　©2009　IEEE.