Dear Gmx users, I am studying the interaction between the tubulin protofilaments arranged in parallel. For this operation, I have considered a tetramer and a dimer from two protofilaments respectively (say PRO-1 and PRO-2), tetramer in PRO-1 and a dimer in PRO-2. I want to move the dimer of PRO-2 over the tetramer of PRO-1 along the length of protofilaments in one axis only, keeping the PRO-1 fixed to its original position. I tried by assuming tetramer as 'reference group' and the dimer as 'pull group' in pull code but the system crashed.
I have succeeded in separating two dimers in Z-axis by using 'distance' geometry. But this case is quite different, as the pulling is not face-to-face but rather a sliding movement over another protofilament. Here, the COM distance between the pull group (dimer of PRO-2) and reference group (tetramer of PRO-1) first decreases and then increases while it moves. How can I simulate this operation by using pull code? Thanks, best regards, Shilpi Chaurasia
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