Dear Gromacs Users, I've done Justin's tutorial regarding PMF/umbrella sampling and now, when approaching my own system I have a couple of questions. (Link to the tutorial here: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html)
My system is comprise of a transport protein (embedded in membrane) and a ligand. The system is positions so that Z axis is the axis on which I've made PMF windows. The next step on this is to run these windows separately and I didn't quite understand why in step-6 of the tutorial it specifies to still use pull_dim = N N Y and pull_rate1 = 0.0. As far as I understood, during the production run we want to sample the Z position. Shouldn't then it use pull_dim = Y Y N ? And what does it mean to the system when we set pull_rate1 = 0.0 ? Does it mean that when pull_dim = N N Y and pull_rate1 = 0.0 it restrains pull_group0 on the Z-axis? This came a bit longish, Thanks in advance, -Shay P.S. Using Gromacs 4.0.7
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