Sorry for my ignorance, since the help manual uses tpr file for the first two steps before running g_spatial, could you please tell me how I should do them without tpr. Also when I just run g_spatial (without the first two steps) I get the distribution of all the anions around cations, so it is not informative.
Thank you so much for all the help On Tue, May 7, 2013 at 2:48 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > I think you can process the trajectories without generating TPR. > > Dr. Vitaly Chaban > > > On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy <venkat...@gmail.com> wrote: > > > Dear gromacs users, > > > > I am analyzing trajectories of an ionic liquid system generated using > AMBER > > MD package. The force field parameters are typical of this IL system and > > not from the existing libraries. Hence, it is difficult for me to > generate > > a tpr file. I understand that running the g_spatial command needs > > pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I > > need tpr file for that. So there is no way of doing g_spatial without a > > tpr file is it? Then how do I generate tpr file for my system? > > > > Thanks for all the help > > -- > > With Best Wishes > > Venkat Reddy Chirasani > > PhD student > > Laboratory of Computational Biophysics > > Department of Biotechnology > > IIT Madras > > Chennai > > INDIA-600036 > > -- > > 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 > > > -- > 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 > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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