Hi all, I am working on steered molecular dynamics and In that I would like to pull the ligand ( already in complex with protein) away from the reference amino acid ( which I've selected so that I can direct the ligand to get closure to my desired amino acid residue). Now the thing is when I used VMD to assign the direction, The desired direction of mine is not along the proper x, y, or in Z axis. So my question is how can i specify the direction in a situation like this. I've seen in other discussions people have used pull_vec. How can I get the values of the pull_vec. Kindly help me . thanks in advance
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