> > Hi Justin, yes the intention is to pull the dimer apart within the plane of > the bilayer. I've ran a few more tests changing a few of the parameters and > got to one set that pulls my dimer apart apparently in a "friendly" way, I > mean, using g_dist to monitor the COM distances I got an increment of 0.4 nm > for a 500ps simulation. Below is my set of parameters. I have a few > questions though. I don't seem to understand the relation between pull_k1 > and pull_rate1. I am sorry if that sounds like a silly question, but I > thought that the rate of pulling would be determined by the force constant > applied and the vector selected.
One other question is regarding a future application. I intend to calculate the free energy of dimerization of my dimer. Using g_wham I would be able to get that, right? Then I got a little confused again, for in a tutorial that exaplains this procedure but using two argon molecules, there is a constraint set between both atoms, and that is coupled to the lambda value. I kind of understand that way of calculating free energy, since it is similar to fep, where is calculate along reaction coordinates. Well, I would really appreciate if someone could give me a reference or any indication on reading material. Anyway, my set of parameters: ; Pull Code pull = umbrella pull-geometry = direction pull_dim = Y Y N pull_nstxout = 10 pull_nstfout = 1 pull_ngroups = 1 pull_group0 = r_1-30 pull_group1 = r_31-60 pull_vec1 = 1 1 0 pull_init1 = 0.0 pull_rate1 = 0.05 pull_k1 = 30 pull_constr_tol = 1e-06 pull_pbcatom0 = 0 pull_pbcatom1 = 0 Fabrício Bracht > > Ragnarok sdf wrote: > > 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. > > > > So the goal is to pull the dimer apart, within the plane of the bilayer? > > > 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 > > With a pull rate of 0, nothing is going to get pulled apart. With umbrella > pulling and a pull rate of 0, the distance between the two groups is going > to be > restrained at its initial value, as I understand it. > > > 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 > > With DPPC as the reference, then pulling would occur between the COM of the > pulled group and the COM of the bilayer. If they lie at the same place > (i.e., > protein dimer centered within the bilayer), I don't think this will work. > > > 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 > > COM pulling should indeed be applied to the center of mass of whatever you > are > trying to pull on. > > If you're trying to separate a dimer, I would try setting pull_group0 = > Protein1 > and pull_group1 = Protein2 (and apply a pull rate > 0). Just a guess worth > trying; I'm still figuring my way through the pull code for a few things, > too :) > > -Justin > > > 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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