I am trying to learn how to use the pull code to separate a dimer. I have read gromacs 4 manual and a tutorial I found on CSC, but it seems I still haven´t got the knack. My system is consisted of a dimer inserted into a membrane lipid bilayer. I have included the following lines into my mdp parameter file.
pull = umbrella pull-geometry = direction pull_dim = Y N N pull_nstxout = 10 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = DPPC pull_group1 = r_31-60 pull_vec1 = 1 0 0 pull_init1 = 0.0 pull_rate1 = 0 pull_k1 = 1000 Since I am trying to separate the two structures I thought about using the DPPC membrane as a reference structure for the pull, since my attemps with the monomer as a reference struture went with nothing happening whatsoever. Is it correct to use such a long series of aminoacids as a pull reference, i.e., gromacs will understand that tha pull should be in the center of mass, right? What does the manual mean with "grompp normalizes the vector"? Is this how I should procede to separate my dimer? Thank you in advance Fabrício Bracht
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