[gmx-users] PBC correction to visualize a protein-membrane structure

Juan Munoz-Garcia juan.munoz-garcia at bioch.ox.ac.uk
Mon May 19 11:36:53 CEST 2014

Dear Justin,

you’re right. The problem was the system was not center properly in the initial .gro file. Now it works.

Thank you very much.

Juan C.

On 5/17/14, 5:49 AM, Juan Munoz-Garcia wrote:
> Dear Mark,
> I’ve used numbers. Just indicated them as x_box/2, etc to be clearer.

There are two possibilities:

1. You built the system wrong and trjconv can't fix it.  Without the full
sequence of commands used to build the system, no one can provide any advice
here.  Providing an image that shows the unit cell ("pbc box" in the Tcl window
in VMD) can also be informative in this regard.

2. This is a PBC issue that should be resolvable, probably within a few
iterations of trjconv.  See
  Often times, it helps to start with a new .tpr file that has the system
centered properly when remove jumps, etc.

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