[gmx-users] Mirror xtc-grp
johnny.lu128 at gmail.com
Fri Sep 5 18:16:37 CEST 2014
sorry for asking that question.
trjconv -f mixed.xtc -o mixed.mirror.xtc -s mixed.tpr -pbc mol fixed that.
On Fri, Sep 5, 2014 at 11:29 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> 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 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.
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