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.<br>My system is consisted of a dimer inserted into a membrane lipid bilayer. I have included the following lines into my mdp parameter file.<br>
<br>pull = umbrella<br>pull-geometry = direction<br>pull_dim = Y N N<br>pull_nstxout = 10<br>pull_nstfout = 1<br>pull_ngroups = 1<br>pull_group0 = DPPC<br>pull_group1 = r_31-60<br>pull_vec1 = 1 0 0<br>pull_init1 = 0.0<br>
pull_rate1 = 0<br>pull_k1 = 1000<br><br>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?<br>
Thank you in advance<br>Fabrício Bracht<br>