[gmx-users] Mirror xtc-grp

[Johnny Lu]

Hi.

Running a protein, ions, and water in a periodic rhombic dodecahedron in
gromacs 4.6.6.

.gro file has protein, ions, and water.
.trr file saves only the protein, as defined by xtc-grps.

In the .gro file, I manually deleted all SOL and ions, change #atoms in
first line, and didn't change the last line, which seems to be the box
definition.

Viewing the trajectory in vmd shows that the coordinates seem not correctly
mirrored.
Some of the bonds go from one end to another end of the protein.

How to fix this? And, what is the normal and correct way to fix this?

Thank you again.