Hi Dmitri, Better to start a new thread for a new issue. It would also help if you give an equation for the Lindemann parameter. Is it really about fluctuations in the intermolecular distance, or in the intramolecular distance? The first would be a bit tough. For the latter you want to have a look at g_rmsdist. It can produce a matrix of distance fluctuations, which you could postprocess.
Hope it helps, Tsjerk On Fri, Apr 2, 2010 at 9:10 AM, Dmitri Dubov <ddu...@ngs.ru> wrote: > Hi all, > > One more similar question: > > How can I get (in the quickest way!) any form of the Lindemann parameter for > rather big molecular crystal? > > (I mean averaged relative fluctuations in the intermolecular distance) > >> Well, you could also use g_rmsf with -b and -e, and a suitable index >> file... > >> Cheers, > >> Tsjerk > >> On Thu, Apr 1, 2010 at 6:18 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > >>> Wu Rongqin wrote: > >>>> Dear all, > >>>> How to get the averaged coordinates for a short time range say, 10 ps? > >>>> which utility should be used? > >>> g_traj to extract the coordinates, g_analyze to do averaging. > >>> -Justin > >>>> r. q. > >>> -- > >>> ======================================== > >>> Justin A. Lemkul > >>> Ph.D. Candidate > >>> ICTAS Doctoral Scholar > >>> MILES-IGERT Trainee > >>> Department of Biochemistry > >>> Virginia Tech > >>> Blacksburg, VA > >>> jalemkul[at]vt.edu | (540) 231-9080 > >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > >>> ======================================== > >>> -- > >>> gmx-users mailing list gmx-us...@gromacs.org > >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > > > >> -- > >> Tsjerk A. Wassenaar, Ph.D. > >> post-doctoral researcher > >> Molecular Dynamics Group > >> Groningen Institute for Biomolecular Research and Biotechnology > >> University of Groningen > >> The Netherlands > > -- > > Regards, > > Dmitri mailto:ddu...@ngs.ru > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology 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/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/mailing_lists/users.php
