probably means your trajectory is not continuous enough. I saw the same
thing when I try to fit an ensemble trajectory, which each frame is not
from the previous one. Or if your first frame in your trajectory is not
good looking(or having good rmsd to your target structure), fit option
cannot fit
Hi all,
I am doing duplicate MD simulations with a protein-ligand system.
After processing one trajectory by trjconv with the optioin -pbc nojump, I
still find abrupt jumps (on the scale of nm) in RMSDs and COM distances.
Then I tried -pbc mol -ur compact, which did not work. And then -fit
On 20/01/2012 7:55 AM, Yun Shi wrote:
Hi all,
I am doing duplicate MD simulations with a protein-ligand system.
After processing one trajectory by trjconv with the optioin -pbc
nojump, I still find abrupt jumps (on the scale of nm) in RMSDs and
COM distances.
Then I tried -pbc mol -ur
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