Hi all, I have done this countless time and I've "googled" this a lot. Unfortunately I have a simulation that simply won't behave.
I am trying to visualise (and analyse) a trajectory in VMD after removing the periodic boundary conditions. It is a helical dimer (important, as I need to consider bonds over the box and also two separate peptides separating over the box), in a box of water. During the first frame the dimer is whole in the box.
I have tried many combinations of trjconv with little success. The most logical, as per the Gromacs web site was:
trjconv -f human_npt_0_40ns.trr -s human_npt_0_40ns.tpr -pbc whole -e 2-o firstframe.gro
I checked the first frame - it is present as t=0.000. The protein (dimer) is whole in the box.
trjconv -f human_npt_0_40ns.trr -s firstframe.gro -pbc nojump -o nojump.gro
In VMD this displays lots of very long bonds i.e., passing through the unit cell to the other side - no good. I tried this option again with -center on the protein. Still no good. I tried to centre the protein for the trajectory after -mol nojump. Still wouldn't work. I am technically not sure what has happened here. On a similar simulation of a dimer, from the above two commands I was getting a beautiful trajectory in VMD. This would suggest that my reference file to the -pbc whole is incorrect, it is not.
Short of listing every possible combination of -pbc I will leave this here and hope that someone has some insight into removing tricky periodicity from GROMACS trajectories.
Thanks
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 :)
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
Anthony Nash , I think the workflow mentioned on this website can solve your issue http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
How I can do this?
6.-Fit the resulting trajectory to some (other) reference structure (if desired), and don't use any PBC related option afterward.
This was taken from
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
Dear Justin Lemkul
I have a very basic question on pbc in gromacs. The comment in lysozyme tutorial on pbc of analysis page is
gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc
-pbc mol -center
I always concern about the name noPBC. Here we are considering
pbc, not removing it in this command. so, why noPBC?
I dont know, maybe I got it wrong, my apology.
Can you please write some words for me
on this. Thank you.
It's a rather lazy way of saying "no PBC effects" in the corrected trajectory.
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