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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:
- -center -pbc whole (centering on chain A) - some frames show separation but one chain is out of the box.
- -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.
- -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.
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
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.
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.
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?
Yes, as u said, if viewed in VMD, the system explodes as we proceed forward in the trajectory.