Dear All,
After energy minimization, 100 ps NVT md and 100 ps NPT md (based on the on-line lysozyme tutorial), I have processed a 30 ns production MD (also based on the on-line lysozyme tutorial). Then I load the NPT.gro and the 30ns_production_md.xtc to the VMD, and by VMD I find in the whole 30 ns md, the whole protein molecule has an about 50 degree rotation (the 50 degree occurs gradually in the 15 ns md, not a sudden 50 degree rotation). Is this 50 degree rotation normal or abnormal? If by VMD I want to observe the local conformation changes in the whole 30 ns md, rather than the global 50 degree rotation, will you please tell me which trajectory file I need to load to VMD, and by which command I can get that trajectory file? Best regards. Smith -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
