[gmx-users] trjconv woes (broken molecules)

[Ignacio Fernández Galván]

--- On Tue, 19/2/13, Justin Lemkul <jalemkul at vt.edu> wrote:

> First use:
> 
> trjconv -trans x y z -pbc mol
> 
> This will allow you to reposition the elements of your
> system such that you have an intact structure at the
> origin.  Then use the structure created as your new
> reference structure for further trjconv iterations (removing
> jumps, making molecules whole, etc).

Thank you, but I must be doing something wrong. With -trans x y z -pbc mol the broken molecule is indeed displaced out of the origin, but it remains broken, and further runs of trjconv (passing this new structure with -s or -f) don't seem to help.

I've tried attaching sample files, but the list doesn't like that.

For the record, I've since noticed that -pbc cluster works in gromacs 4.5.5, but not in 4.5.3, so in a machine with the former this appears to work:

$ trjconv -f final.gro -s init.tpr -o tmp.gro -pbc cluster
(select group 2 for clustering)
$ trjconv -f tmp.gro -s init.tpr -o new.gro -pbc mol -center -boxcenter zero -ur compact
(select group 2 for centering)

And my newest finding is that if I define bonds inside the frozen molecule, then I can do without the "-pbc cluster", and just a single "-pbc mol -center -boxcenter zero -ur compact" does what I need, and it joins together in the center the frozen molecule that was initially broken. So, where I would normally just use (simplified case, real case is more complex):

  [atoms]
  1     opls_111  1       SOL              OW             1       -0.834
  2     opls_112  1       SOL             HW1             1        0.417
  3     opls_112  1       SOL             HW2             1        0.417

  [exclusions]
  1 2 3
  2 3

it's better to add:

  [bonds]
  ; type "5" is a dummy bond
  1 2 5
  1 3 5