Dear Sir, Thanks for your patient reply Sir.
With Regards M. Kavyashree On Sat, Jun 11, 2011 at 9:57 PM, Tsjerk Wassenaar <[email protected]> wrote: > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
