[gmx-users] g_select vs trjorder
Dear Tsjerk and Mark Thanks for your time and attention. using g_select -f *.xtc -s *.tpr -n index.ndx -oi -select 'Close to Protein resname SOL and within 0.25 of group Protein' solved my problem. I want to use trjorder -f *.xtc -s *.tpr -n index.ndx -o ordered.pdb -nshell -r 0.25 -na 3 -da 1 to order water molecules according to the smallest distance to atoms in a reference group (protein). Should the results of both of g_select and trjorder be the same? Best regards. -- 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
[gmx-users] g_select vs trjorder
Dear all Which one of g_select and trjorder is the best for obtaining those water molecules being within x nm of protein? -- 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_select vs trjorder
leila karami wrote: Dear all Which one of g_select and trjorder is the best for obtaining those water molecules being within x nm of protein? You will have to define what obtaining means. The tools you've mentioned do different things. With g_select, you obtain index groups that tell you which atoms satisfy the given criteria. With trjorder, the coordinates of those atoms are reordered such that they are listed in sequence in the new trajectory. -Justin -- 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 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
[gmx-users] g_select vs trjorder
Dear Justin Thanks for your reply. I know, with g_select, I obtain index groups that tell me which atoms satisfy the given criteria and with trjorder, the coordinates of those atoms are reordered such that they are listed in sequence in the new trajectory. But g_select gives an output file (size.xvg) and trjorder gives an output file (nshell.xvg). Both of these output files contain number of atoms satisfy the given criteria. In my case these number are not the same at the special frame. Why? -- 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_select vs trjorder
leila karami wrote: Dear Justin Thanks for your reply. I know, with g_select, I obtain index groups that tell me which atoms satisfy the given criteria and with trjorder, the coordinates of those atoms are reordered such that they are listed in sequence in the new trajectory. But g_select gives an output file (size.xvg) and trjorder gives an output file (nshell.xvg). Both of these output files contain number of atoms satisfy the given criteria. In my case these number are not the same at the special frame. Why? From g_select -h: With -os, calculates the number of positions in each selection for each frame. From trjorder -h: With option -nshell the number of molecules within a shell of radius -r around the reference group are printed. Thus the two output files should not be equivalent. -Justin -- 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 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
[gmx-users] g_select vs trjorder
Dear Justin You are wright. The two output files should not be equivalent. If I want to know residue number of water molecules being within x nm of protein, which tool is the best for me? -- 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
[gmx-users] g_select vs trjorder
Dear Justin If I want to know residue number of water molecules being within x nm of protein, for each frame, which tool is the best for me? -- 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_select vs trjorder
leila karami wrote: Dear Justin You are wright. The two output files should not be equivalent. If I want to know residue number of water molecules being within x nm of protein, which tool is the best for me? If you simply want to identify which residues they are, then maybe g_dist -dist, or otherwise using g_select to find OW atoms within whatever your distance is, since the count of OW will be the number of molecules of water within that distance. -Justin -- 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 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
