Hi Justin. So for each window, I would turn pull_rate to zero in order to get a system in equilibrium? And then the lambda value would be equal to each of the sampling distances? How would I justify using this pull_rate and pull_k1 values in order to obtain my pulling trajectory? i.e. is there somekind of standard, or would I need to rely on certain parameters, like rmsf of my protein or area per lipid? Fabrício Bracht
> > Ragnarok sdf wrote: > > 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. > > > > The pull rate is how fast the applied force moves; pull_k1 is the force > constant > of the spring doing the pulling. > > > 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, > > Yes. > > > 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: > > I've yet to find a good tutorial for this purpose. If anyone else knows of > one, > I'd be curious. I've been doing some pulling lately to calculate PMF for > various ligand-binding events. The way I think things need to go is: > > 1. Generate a trajectory of configurations along the reaction coordinate. > 2. Use different configurations as the starting points for independent > simulations in each sampling window. > 3. Use umbrella sampling to restrain these configurations within the > windows. > 4. Calculate PMF from these simulations. > > If anyone else has a better or more complete explanation, I'd like to see > it, > too; the documentation on the subject is a bit thin. > > -Justin > > > ; 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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