Trajectory extraction of multimeric system

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Dear Members,
I have done a dimer simulation and I want to extract its trajectory and visualize in VMD .
I have tried 3 command using gmx_trjconv and obtained the results as follows:

  1. -center -pbc whole (centering on chain A) - some frames show separation but one chain is out of the box.
  2. -center -pbc mol -ur compact (centering on whole protein) - the same results as above method but the frames which show separation , have chains at opposite ends of box with some part of the chain outside the box.
  3. -center -pbc mol -ur compact (centering on chain A) - shows both chains at middle of the box with no separation at all in any of the frames.

Note: Structural conformation of each chain individually remains same in all the 3 cases.

Now, I am not sure which is the correct method of extraction and whether there is any separation in chains or not.

Hi @priyanka

Since no-one more expert has answered your question I will have a go. This is what has worked for me:

System prepared according to the Lemkul tutorials

em_1.gro: Coordinates after initial (steepest descents) minimization. The chains are in their correct relative positions and the complex is in the center of the periodic box.

md_1f_1.gro + md_1f_1.xtc: Structure and trajectory files after MD run
index_1d.ndx: Index file including definition of the complex of interest

Then do:

gmx trjconv -f md_1f_1.xtc -s em_1.gro -n index_1d.ndx -pbc nojump -o tmp_1.xtc << eof

(note that I’m using “-pbc nojump”)
This should give you a new trajectory file with the dimer chains back in the center of the box.

Please let me know whether this does / does not work for you.

Guy Vigers

hello @gvigers
Thank you for the suggestion.
I earlier tried using no jump but , the trajectory when I see in pymol is all scattered. I tried using combinations of no jump with -fit and also with -pbc whole, -center , etc. but using no jump itself is making the atoms scattered as below.

The scattering increases with time for futher frames.

Hi @priyanka

That looks very odd! If you look at the original trajectory into VMD (not Pymol) does it look OK? Or is your system exploding during the MD run?

hello @gvigers
Yes, as u said, if viewed in VMD, the system explodes as we proceed forward in the trajectory.

Did you find a solution for this issue? I am facing a similar problem.


Hello Zhaleh

I used gmx trjconv -pbc mol -ur compact -center (centering was done on one of the chains in dimer). This worked out for me. Try it once.