Hi Kavya, >> It is absolutely necessary that the molecules be whole, and in the >> case of multimers, correctly assembled. > > But if there is only one polymer (protein) with water in the system > then also is it necessary to use nojump or mol in trjconv?because > in one of the mails - > > http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html > > there was a discussion regarding this topic. So I wanted to > ensure regarding that aspect. Molecule after simulation > crosses the box boundary in the simulation I have done, So > if I processed analyzing with the native .xtc file there will be > a problem? But in this case its a single intact protein molecule > in water.
That post concerns -pbc nojump. My reply to you was about having molecules in one piece. They're different things. Gromacs nowadays doesn't care about molecules being whole in the trajectory file, and happily writes them in pieces. So you can't be confident you can use the trajectory as is. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
