I am trying to pull apart two dimers of tubulin protein joined together, to form two separate dimers by steered molecular dynamics using Pull code. The objective is to separate the dimers by pulling along one axis only (Y axis). I ran the simulation for 25 ps and it accomplished well but while visualizing the trajectory in VMD, in the very beginning (first frame), dimers are at distance which is much greater than expected. I expected that in first frame they should not have separated too much (i.e. in just 1 ps, they are at greater distance) I guess this is unusual. Please let me know where I am doing wrong? I have used the following pull code:
pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_init1 = 0.0 pull_ngroups = 1 pull_group0 = dimer_ref ; reference group (based on index file) pull_group1 = dimer_pull ; pull group pull_rate1 = 0.1 pull_k1 = 1000 pull_nstfout = 10 pull_nstxout = 10 best regards, Shilpi Chaurasia
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