[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

[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

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

[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

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

[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

[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

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