[gmx-users] on VMD analysis of the gromacs production MD

Brett brettliu123 at 163.com
Sun Jul 12 02:45:41 CEST 2015

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.


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