Sounds like a trjconv problem, not a g_spatial problem to me. You should center only the group that makes sense for your SDF -- you probably want to pick a single cation for this (then, separately, do another run selecting a single anion; each will be used to generate a separate SDF). Then output the whole system. This should work. If not, then I suggest that you start a new post with a relevant title and figure out what you are doing wrong with trjconv ... you'll need to post actual commands there with associated error messages.
If you want to output only a portion of the system in your step 1, then you need to provide a -s input with the same number of atoms in step 2. Nevertheless, just use the whole system for trjconv for now since it should work. Regarding your "seeing the whole distribution" for ANI from g_spatial output in VMD, I don't understand what you see and what you expect/want to see. Try posting a figure somewhere online and post with its location and a description of what you want to obtain. If you want the distribution of all C cations around the average of all A anions, then you need to create a trajectory that is A times as long as your real trajectory and reorder the coordinates so that each anion has a turn being residue number N. Then center your whole trajectory about residue N. This is a hack, but it works for me and I think is what you want. Also, the tool g_sdf does this on its own so you might look online for an older version of it. I found it less useful than g_spatial for my purposes, but some users have found it to be the perfect tool. Chris. -- original message -- Yes, trjconv works without tpr. Thanks for that. I want to see the distribution of anion around cation. Is it not possible to see an averaged spatial distribution of all anions around all cations? Do I need to make a selection of a single cation molecule? I did the selection of a single cation molecule which is approximately at the center of the box and did the following step 1: trjconv -s 1md.pdb -f 11md_gro.pdb -o 11md_gro_mod.pdb -center -ur compact -pbc none when it asked for group for centering and output, I selected the whole system for both. step 2: trjconv -s 1md.pdb -f 11md_gro_mod.pdb -o 11md_gro_mod1.pdb -fit rot+trans when it asked for group for least square once again I selected the whole system I selected the whole system as a previous discussion http://lists.gromacs.org/pipermail/gmx-users/2010-May/050879.html suggested the same because of an error that was happening in step 2. *Fatal error: Index[2385] 2410 is larger than the number of atoms in** the trajectory file (2409). * Since I was getting the same error if I made any form of selections in the first two steps, I output the whole system. step 3: g_spatial. and used ANI as group to generate SDF and a single cation residue as the group to output coords When I loaded the resultant cube in vmd I could see the whole distribution. Where am I going wrong? -- 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
