Hi, there is no tool to do that. Trajectories assume to have the same number of atoms per frame. What you can do is use g_order (it gives you the water sorted by distance and the number of water within .5nm) or g_select (it can give you an index file with the atoms within .5nm for each frame)
Roland On Mon, May 9, 2011 at 10:50 AM, maria goranovic <mariagorano...@gmail.com>wrote: > Dear experts > > I have a protein simulation in a water box. I now want to write a > trajectory containing only the protein, and water molecules within 5 > Angstroms of the protein, with the water list being updated each time step. > How can one do this? Appreciate the help > > -- > Maria G. > Technical University of Denmark > Copenhagen > > -- > 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 > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
-- 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
