[gmx-users] g_rdf problem
Hi, I am using gromacs_4.0.7 to calculate the Scattering Intensity as a function of scattering vectors(q) using g_rdf -sq command . But, I found that there is no way that one can increase/decrease the grid spacing for structure factor calculation. I tried using -bin option , but that does not change anything as that only works for changing bin-width for Radial distribution functioncalculation. If some one can point me out any way out of changing the grid spacing for structure factor, that will be very helpful. Sanku-- gmx-users mailing listgmx-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
Re: [gmx-users] g_rdf problem
avinash kumar wrote: Dear all, I am having a problem in running some post analysis commands like g_rdf on my computer . When my simulation is complete I type in the following command to calculate the radial distribution function for the system " g_rdf -f traj.trr -s topol.tpr -o rdf.xvg -b 0 -e 20 " and the program gives a message like this probably installation issues. which version and how was it compiled on which platform? :-) G R O M A C S (-: Gallium Rubidium Oxygen Manganese Argon Carbon Silicon :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_rdf (-: Select a reference group and 1 group Opening library file /usr/share/gromacs/top/aminoacids.dat Group 0 ( System) has 648 elements Group 1 ( SOL) has 648 elements Select a group: 1 Selected 1: 'SOL' Select a group: 1 Selected 1: 'SOL' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 After displaying this line the program does nothing further . I checked for the installation of g_rdf and found it to be installed . My simulation was completed and for command like "trjconv" can read all the frames . Then why is "g_rdf" command failing to read all the frames? eagerly waiting for a reply. Avinash Kumar 3rd year undergraduate IIT Khragpur,India Mechanical Engineering Department ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] g_rdf problem
Dear all, I am having a problem in running some post analysis commands like g_rdf on my computer . When my simulation is complete I type in the following command to calculate the radial distribution function for the system " g_rdf -f traj.trr -s topol.tpr -o rdf.xvg -b 0 -e 20 " and the program gives a message like this :-) G R O M A C S (-: Gallium Rubidium Oxygen Manganese Argon Carbon Silicon :-) VERSION 3.3.1 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2006, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) g_rdf (-: Select a reference group and 1 group Opening library file /usr/share/gromacs/top/aminoacids.dat Group 0 ( System) has 648 elements Group 1 ( SOL) has 648 elements Select a group: 1 Selected 1: 'SOL' Select a group: 1 Selected 1: 'SOL' trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 After displaying this line the program does nothing further . I checked for the installation of g_rdf and found it to be installed . My simulation was completed and for command like "trjconv" can read all the frames . Then why is "g_rdf" command failing to read all the frames? eagerly waiting for a reply. Avinash Kumar 3rd year undergraduate IIT Khragpur,India Mechanical Engineering Department ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
