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I energy minimized the a protein complex that consist of 2 chains. i performed the energy minimization and npt/nvt equilibration using the same parameters as described in the lysozyme tutorial. In the final frame of npt.trr file both the chains appear to be very distant.
instead of getting the coordinates of the last frame i wanted to get the average coordinates in the npt.trr so i used the following command
gmx traj -f npt.trr -s npt.tpr -oxt npt2.trr -cv npt2.pdb -b 1-e 100. but i am getting a borken pdb file. I have aligned the initial stricture(green) with the averaged npt structure(cyan). i am confused as to why this is happening . the problem appear to be in the starting couple of residues of Chain B.
I would guess this has to do with jumps over the periodic boundary - that will cause problems when trying to get average coordinates.
Does it help if you do:
gmx trjconv -s npt.tpr -f npt.trr -pbc nojump -o npt_nojump.trr
gmx traj -f npt_nojump.trr -s npt.tpr -oxt npt2.trr -cv npt2.pdb -b 1-e 100
?
thank you. I tired -pbc nojump but still faces the same issue but it was resolved once i did the rot+trans fit