[gmx-users] Mirror xtc-grp

Johnny Lu johnny.lu128 at gmail.com
Fri Sep 5 17:29:14 CEST 2014


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

Viewing the trajectory in vmd shows that the coordinates seem not correctly
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.

More information about the gromacs.org_gmx-users mailing list