Dear Daniela, > If the molecule you want to analyse is a single molecule, the > jumping of > box boundaries does not matter and the analysis tools take that into > account. But if your molecule is a complex of two or more separate > subunits, you might want to remove jumps over the boundaries to > reassemble the complex again, e.g. to measure the minimum distance to > the periodic images (and not to the subunit, which should be very > nearby). > > What I actually found with trjconv -pbc nojump was, that two > conditionsapply if you want to remove jumps: 1) the trajectory has > to start at the > initial frame and be continuous; 2) the tpr-file should correspond to > the initial conformation. If these conditions weren't fulfilled, > one of > the subunits was rotated and the complex was reassembled > incorrectly - > although the box was rectangular. > This incorrect rotation seems to be a weird bug, probably the > referencing to the tpr-structure is a special case-treatment and not > robust to various setups...?
Thank you very much for this information. Could you specify in more details what do you mean when you Could it be residials of a polypeptide/protein chain or you mean something else? All the best, Maxim. > > Success and best regards, > Daniela > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
