[gmx-users] Centering using trjconv

[Mitchell J Stanton-Cook]

Hello All.

I am simulating t4 lysozyme with NAG. I have added a short peptide label
to lysozyme which binds calcium ions.

During the simulation there is some drift. I am attempting to re-center
the protein+label+NAG+Ca ion.

I am using trjconv and have setup an index file that contains only these
atom groups (protein+label+NAG+Ca ion).

First, I tried just centering using:

trjconv -f d61_15_25ns.gro -s md_initial.tpr -n analysis.ndx -center
tric -o test.pdb

This center's, however NAG and the calcium ion are not in the expected
positions.

Using:

trjconv -f d61_15_25ns.gro -s md_initial.tpr -n analysis.ndx -center
tric -o test.pdb -pbc whole

The ions and NAG are where they are expected, however, the protein has
been split.

Using inbox results in something similar.

Does anyone know how to do this?

Cheers Mitch