Have you performed it in GROMACS? And what do you mean by the "basin area"? The violet region?

If Yes.

Open shamlog.log

Search "Minima sorted after energy"

- The lines under it are the index vs energy data, arranged in ascending order.

- If highest energy (violet) is concerned, choose the last index; for lowest energy (red), choose first index

Open bindex.ndx

Search for that index (in square brackets; for eg. [ 541 ])

- The values listed under that index, represent the frame values.

- Count all the frames corresponding to that index, divide it by total no. of frames x100

- That's it.

If you are not using Gromacs gmx sham, I am not very sure.

Uddipta Ghosh Dastidar iI am working on Gromacs,and the basin area means the whole groove(minima conformations).

is there any commands to do it rather than manually.