Hi Leila, 2.xtc should contain all that you want. My point was that you shouldn't need to separate protein/dna and solvent into two trajectories to be combined later. Note that this only concerns visualization. You can do distance and H-bond calculations on the original trajectory, as the relevant tools know how to deal with PBC.
Cheers, Tsjerk On Wed, Oct 27, 2010 at 12:01 PM, leila karami <karami.lei...@gmail.com> wrote: > Dear Carsten and David and Tsjerk > > Thanks for your time and attention > > My purpose of these questions is to find a way that 1) close two separated > strand of dna (in my case only –pbc nojump fix it) and also 2) water > molecules to be put in interface of between protein and dna. Because I want > to survey interfacial water molecules and dynamics of water mediated > hydrogen bonds. > > -- > 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 > -- 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
