An update on this. I got the following to work: 1. use a vmd script closest.tcl (available on the vmd pages) to select closest N waters, and write a pdb file for each frame.
2. however, the above pdb files have different residue numbers for the water molecules for each frame because it is not the same N waters each frame. So use editconf to convert the pdbs to gros with the -resnr 1 option 3. concatenate the frames using trjcat ( -cat option) 4. make the correct time spacing using trjconv. (-timestep) The method is kinda tedious, but the final result is a trajectory of the protein with closest N-waters updated every step. Good enough for my analysis. On Tue, May 10, 2011 at 12:38 PM, Thomas Evangelidis <teva...@gmail.com>wrote: > A work around will be available in the future as a plugin for VMD. > > For your reference read these threads: > > http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/14140.html > > http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/13217.html > > > On 10 May 2011 03:12, Roland Schulz <rol...@utk.edu> wrote: > >> >> >> On Mon, May 9, 2011 at 6:28 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: >> >>> On 10/05/2011 12:50 AM, maria goranovic 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 >>>> >>> >>> g_select is useful for "dynamic" selections of this type. g_select >>> -select "help" can give examples and such. >>> >>> I'd hope it's been designed so that then using trjconv to extract such >>> selections works, but I can't think how, having not ever tried. >>> >> g_select writes out one index group per time frame. But trjconv can't use >> a different index group for each frame. Thus it can't be used to write out a >> trajectory with those atoms for each frame. Part of the problem is that the >> trajectory format doesn't support different number of atoms for different >> frames. >> What is possible is writing a small script around trjconv to produce one >> gro/trr file per frame with only those atoms. >> >> Roland >> >> >>> Mark >>> -- >>> 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 >> > > > > -- > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tev...@bioacademy.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > -- > 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 > -- Maria G. Technical University of Denmark Copenhagen
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