[gmx-users] inquiring for solving trjconv problems

[Mehdi Bagherpour]

hello justin

I used *make_ndx -f md.tpr:

  0 System              : 35194 atoms
  1 DNA                 :  1012 atoms
  2 MG                  :     4 atoms
  3 CL                  :    29 atoms
  4 K                   :    51 atoms
  5 Water               : 34098 atoms
  6 SOL                 : 34098 atoms
  7 non-Water           :  1096 atoms
  8 Other               :     4 atoms
  9 MG                  :     4 atoms
 10 CL                  :    29 atoms
 11 K                   :    51 atoms
 12 Ion                 :    80 atoms
 13 MG                  :     4 atoms
 14 CL                  :    29 atoms
 15 K                   :    51 atoms
 16 Water_and_ions      : 34178 atoms

 nr : group       !   'name' nr name   'splitch' nr    Enter: list groups
 'a': atom        &   'del' nr         'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr        'splitat' nr    'h': help
 'r': residue         'res' nr         'chain' char
 "name": group        'case': case sensitive           'q': save and quit
 'ri': residue index

 > 1

Copied index group 1 'DNA'

 17 DNA                 :  1012 atoms*

then I used from bellow command:

*trjconv -s md.tpr -f md.xtc -n index.ndx -o md_1.xtc -center*

and then:

*trjconv -s md.tpr -f md_1.xtc -n index.ndx -o md.pdb -pbc mol -ur compact*

but problem is not fixed.