Duplicated frames

User discussions
1

Hello,

I have a trajectory obtained by a colleague by concatenating several .dcd files (with catdcd) from a simulation with NAMD. I converted the dcd to a trr file either with VMD or mdconvert (from MDTraj) and I see that the trajectory has more frames than expected, that makes me think that the additional are duplicated frames.

Is there any way to check a trajectory directly for duplicated frames and eliminate them?

Best and thanks in advance.
-Yasser

2

Hi,
gmx trjcat can help you to eliminate double time frames in the concatenate process. I do not know if it does the work on an already concatenate trajectory.
\Alessandra

3

gmx check will tell you about frame intervals and if there are doubles. Note that you can use catdcd to produce .trr files without duplicate frames.