Hi Sunyeping, Besides using the scripting language in pymol, you might want to consider the experimental PyMOL extension created by the PyMOL Fellows (me and Paul Smith, https://pymol.org/fellowship/). The extension relies on the MDAnalysis package and so far includes RMSD as an example. Here is the link to the right github branch https://github.com/bieniekmateusz/pymol-open-source/tree/fellows_mp_2018
If you compile it, you can use the RMSD this way: mda_load systemX.gro mda_load_traj systemX.xtc mda_rmsd Kind Regards, Mateusz On Mon, 19 Aug 2019 at 12:53, sunyeping via PyMOL-users < pymol-users@lists.sourceforge.net> wrote: > Dear everyall, > > I loaded a molecular dynamics simulation trajectory (A.xtc) of 5000 frames > and a reference structure (B.pdb) into pymol. I wish to get the rmsd value > between each state of the MD simulation trajectory and the > reference structure, but I don't know how. I can use the align command as: > "align A, B", but this only gives one rmsd value. Could you tell me how to > get the rmsd value between each state of the MD simulation trajectory and > the reference structure? > _______________________________________________ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
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