Hi, I am trying to pull the first from the last amino acid of a protein to completely unfold the protein in the X direction. I chose the middle amino acid as the reference, and the groups get pulled in the same direction or opposite direction (which is what I want) depending on the trial. I am trying to find a definite method to completely unfold it.
I define a different vector (pull_vec1 and pull_vec2) with +x and -x values and that does not even pull the protein I tried using only pull_group1 and pull_group2, without a reference, and neither groups get pulled. I chose different references, I do have some success but I don't think it is the best way to do it. How do I pull the N and C terminal apart, by simultaneously pulling them in opposite directions?Why is my vector definition wrong? This is my pull code: pull = umbrella pull_geometry = distance pull_dim = Y N N pull_start = yes pull_ngroups = 2 pull_group0 = Chain-C pull_group1 = Chain-B pull_group2 = Chain-A %pull_vec1 = -31 0 0 %pull_vec2 = 31 0 0 pull_rate1 = 0.002 pull_k1 = 1000 pull_rate2 = 0.002 pull_k2 = 1000 Thanks! -- *"Every sentence I utter must be understood not as an affirmation but as a question." - Niels Bohr*
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