Hi there,
I am simulating an all-atom system containing a polymer molecule in water. But after seeing the trajectories, many of the atoms seems to be shifted during the whole trajectory. I have already tried trjconv with centering and no jump options but the problem doesn't resolve. One can still see the large lines in the whole trajectory frame. I have kept the image for reference.
Thanks in advance.
Rahul Sahu
Use this command:
gmx trjconv -f xtc -s tpr -ur compact -pbc mol -o xtc
-pbc mol will bring the com of the molecules inside the box, and -ur compact will compact the box.
please do centering in the next command.
1 votes
1 thanks
- Badges
- Science topic
More Desh Deepak Yadav's questions See All
Similar questions and discussions