trjconv: broken molecules with -pbc whole; molecules out of box with -pbc com
When trying to put an amino acid in the center of the box with trjconv,
problems occur for moving the water inside this image box.
The -pbc whole function broke the molecules at the borders, and gave the same
configuration as -pbc inbox (diff of confs from both commands gives zero output)
The -pbc com worked better, but placed a single water molecule outside the box!
#11 Updated by Berk Hess about 13 years ago
I have fixed all problemsin 3.3 and CVS.
I have fixed the center problem by adding a -boxcenter option,
as in the development version.
The -pbc com_res forgot to put the last residue in the box.
I also found and fixed more problems.
-pbc com_mol made a mess of the system
com_res and com_mol put the center of geometry in the box,
I changed this to com
I have added rm_pbc for com_res and com_mol
I have reordered and renamed the -pbc options:
first mol, res and atom
the -pbc whole option now only does rm_pbc, no inbox.
com_res and com_mol only worked for -ur rect, fixed
this to work with tric and compact.
I think this is a big improvement to trjconv.
-pbc mol or res is what one would usually want.