Dear gromacs users I read g_spatial tool of gromacs 4.5 manual. I have many questions.
There are in the manual: USAGE: 1. Use make ndx to create a group containing the atoms around which you want the SDF 2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none 3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans 4. run g spatial on the xtc output of step #3. 5. Load grid.cube into VMD and view as an isosurface. In the step 2, [-center tric -ur compact -pbc none] is true or [-center -ur compact -pbc none]? In determination of SDF, there are 2 groups: for example; SDF of the first (1) group around second (2) group. In the step 2 of above usage, we should select two groups of the index file, for centering and for output. How to select these groups? group 1 and then group 2 or group 2 and then group 1? Or there is another case (all of the system). In the step 3 of above usage, we should select two groups of the index file, for least squares fit and for output. How to select these groups? group 1 and then group 2 or group 2 and then group 1? Or there is another case (all of the system). In the step 4 of above usage, we should select two groups of the index file, to generate SDF and to output cords. How to select these groups? group 1 and then group 2 or group 2 and then group 1? Or there is another case. Please answer my question exactly with determining group numbers in the each step. Any help will highly appreciated. Best regards -- 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
