Well, but the problem is how would I constrain such a large structure. I mean, I would have to choose certain pairs of atoms to monitor the constrain, or would I be able to set a constrain only between two atoms? I imagine that this procedure would be very similar to the argon argon PMF tutorial, right? Fabrício Bracht
> > > I personally prefer using a constraint instead of an umbrella potential. > This avoids choosing a force constant and avoid the WHAM procedure. > > You can also start the re/constrained simulation from the last > configuration > at the previous distance. But this is not convenient if you want to run > multiple > simulations simultaneously. > In both methods checking the convergence of the re/constraint force is > critical. > > Berk > > > > 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 > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- > > ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! 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