Multimeric systems are difficult for any PBC routine in any software to deal with.  The quickest solution is probably (1) make the molecules whole as you have done and then (2) center on interfacial residues belonging to one monomer, via a custom index group.  Doing this will put the interface of the dimer at (or at least, extremely close to) the center of the box, with both monomers in the unit cell.

Multimeric systems are difficult for any PBC routine in any software to deal with.  The quickest solution is probably (1) make the molecules whole as you have done and then (2) center on interfacial residues belonging to one monomer, via a custom index group.  Doing this will put the interface of the dimer at (or at least, extremely close to) the center of the box, with both monomers in the unit cell.

Thanks Justin, I will give this a go. I suspected it was due to the multimeric nature of the system. 

It is, and there's never a recipe.  I did some work on a heterodimeric protein complex, bound to dsDNA, with two ligands and two coactivator peptides.  Two domains had Zn ions bound.  Imagine chasing that around via PBC.  I had five different simulation setups, and had to use 3-4 different trjconv sequences to get everything re-imaged :)

Not my idea of fun! 

I'll let you know how it goes. Thanks again. 

Hi Anthony,

I hope you are not struggling with this problem anymore since it is an old post. But I think in future if above things doesn't work, you can try below mentioned trjconv command.

trjconv -f *.trr -s *.tpr -o *.trr -b 0 -e 2 -ur compact -pbc mol

If you are visualizing through VMD you can virtually upgrade the view to show periodic images of the system in case if the molecule is broken.

Cheers!

When I use this command line:  trjconv -f *.trr -s *.tpr -o *.trr -b 0 -e 2 -pbc mol, I must select protein-H or another option? Best regards !

What works for me  (keeping only the protien) is the following:

trjconv -f $traj.trr -s $template.gro -pbc nojump -o $traj2-pbc.xtc

trjconv -f $traj2-pbc.xtc -s $template.gro -fit rot+trans -o $traj2-pbc-rt.xtc

Melchor, thanks for prompt reply. Please, what is template.gro? first frame? It is noteworthy that my system is homodimer protein.

Best regards.

Not necessarilly the first frame, althoulght it can be. It can be last frame coming from MD also. But I usually use the last frame coming from the heating or miniization runs.

Melchor, I have used this command file to generate rmsd.xvg

trjconv -f *.trr -s *.tpr -b 0 -e 2 -o firstframe.gro

trjconv -f *.trr -s firstframe.gro -pbc nojump -o traj2-pbc.xtc

trjconv -f traj2-pbc.xtc -s firstframe.gro -fit rot+trans -o traj3-pbc-rt.xtc

rms -f traj3-pbc-rt.xtc -s firstframe.gro -o rmsd.xvg

What you think?

I guess it should work. Try to represent traj3-pbc-rt.xtc over the firstframe.gro in vmd to see if the pbc conditions have been removed properly. Independently of that the rmsd command should work fine, as it is a gromacs command it can work with pbc conditions or not, the proposed "treatment" is just to have a good view in vmd, nothing else. In fact even having a "bad" view in vmd its own rmsd calculation tool should work properly.

Thank you all, your discussion helps me to resolve the same issue occuring in my system.

Help, please...

https://www.researchgate.net/post/Problemas_con_solvatacion_automatica_en_VMD