GROMACS version: 2019.4
GROMACS modification: No
I have a protein complex on which I ran some REMD and I want to solve PBC issues before analysis.
However, no matter what I tried, one of the proteins still jumps out of the box.
Firstly I make the system whole with:
$gmx trjconv -f md.xtc -s nvt_298.15.tpr -pbc whole -o whole -n index.ndx
This makes the molecules whole, although both proteins in the complex “jump around”.
I have then centered the system on an interfacial residue of one of the complex partners with:
$gmx trjconv -f whole.xtc -o whole_center.xtc -s firstframe.gro -center yes -n index.ndx (the first frame is whole with the complex bound).
I have now one of the partners in the center of the box (the one for which I have centered the interfacial residue) while the other jumps occasionally across.
At this stage, no matter what I try, I cannot solve the second protein from jumping.
I can center (as done in the previous stage) on an interfacial residue belonging to the second protein but this just reverses the problem (with the first one jumping across).
How to reimage the second protein, while keeping the coordinates of the first binding partner that is centered? I have tried clustering, as well as clustering+re-centering…
-pbc nojump ( $gmx trjconv -f whole_center.xtc -s firstframe.gro -pbc nojump -o whole_center_nj.xtc -n index.ndx) makes a mess; with atoms displaced all over the place - but maybe there is something else I can do?
Any help will be greatly appreciated. Thank you in advance for your time.