probably means your trajectory is not continuous enough. I saw the same thing when I try to "fit" an ensemble trajectory, which each frame is not from the previous one. Or if your first frame in your trajectory is not "good looking(or having good rmsd to your target structure)", fit option cannot fit the rest to such starting structure.
On Thu, Jan 19, 2012 at 4:32 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 20/01/2012 7:55 AM, Yun Shi wrote: > >> Hi all, >> >> I am doing duplicate MD simulations with a protein-ligand system. >> >> After processing one trajectory by trjconv with the optioin -pbc nojump, >> I still find abrupt jumps (on the scale of nm) in RMSDs and COM distances. >> >> Then I tried -pbc mol -ur compact, which did not work. And then -fit >> progressive on protein atoms, which again did not completely eliminate >> those jumps in protein atom RMSDs. >> >> I wonder if I have not used the right option? >> > > There's a suggested workflow here http://www.gromacs.org/** > Documentation/Terminology/**Periodic_Boundary_Conditions<http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions>which > you can adapt to your needs. > > Mark > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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