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<br><br>> Date: Sat, 22 Aug 2009 20:01:19 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Re: Pull to separate dimer<br>> <br>> <br>> <br>> Ragnarok sdf wrote:<br>> > Hi Justin, yes the intention is to pull the dimer apart within the<br>> > plane of the bilayer. I've ran a few more tests changing a few of<br>> > the parameters and got to one set that pulls my dimer apart<br>> > apparently in a "friendly" way, I mean, using g_dist to monitor the<br>> > COM distances I got an increment of 0.4 nm for a 500ps simulation.<br>> > Below is my set of parameters. I have a few questions though. I<br>> > don't seem to understand the relation between pull_k1 and<br>> > pull_rate1. I am sorry if that sounds like a silly question, but I<br>> > thought that the rate of pulling would be determined by the force<br>> > constant applied and the vector selected. <br>> > <br>> <br>> The pull rate is how fast the applied force moves; pull_k1 is the force constant <br>> of the spring doing the pulling.<br>> <br>> > One other question is regarding a future application. I intend to <br>> > calculate the free energy of dimerization of my dimer. Using g_wham I <br>> > would be able to get that, right? Then I got a little confused again, <br>> <br>> Yes.<br>> <br>> > for in a tutorial that exaplains this procedure but using two argon <br>> > molecules, there is a constraint set between both atoms, and that is <br>> > coupled to the lambda value. I kind of understand that way of <br>> > calculating free energy, since it is similar to fep, where is calculate <br>> > along reaction coordinates. Well, I would really appreciate if someone <br>> > could give me a reference or any indication on reading material. Anyway, <br>> > my set of parameters:<br>> <br>> I've yet to find a good tutorial for this purpose. If anyone else knows of one, <br>> I'd be curious. I've been doing some pulling lately to calculate PMF for <br>> various ligand-binding events. The way I think things need to go is:<br>> <br>> 1. Generate a trajectory of configurations along the reaction coordinate.<br>> 2. Use different configurations as the starting points for independent <br>> simulations in each sampling window.<br>> 3. Use umbrella sampling to restrain these configurations within the windows.<br>> 4. Calculate PMF from these simulations.<br>> <br>> If anyone else has a better or more complete explanation, I'd like to see it, <br>> too; the documentation on the subject is a bit thin.<br>> <br>> -Justin<br>> <br><br>I personally prefer using a constraint instead of an umbrella potential.<br>This avoids choosing a force constant and avoid the WHAM procedure.<br><br>You can also start the re/constrained simulation from the last configuration<br>at the previous distance. But this is not convenient if you want to run multiple<br>simulations simultaneously.<br>In both methods checking the convergence of the re/constraint force is critical.<br><br>Berk<br><br>> > ; Pull Code<br>> > pull = umbrella<br>> > pull-geometry = direction<br>> > pull_dim = Y Y N<br>> > pull_nstxout = 10<br>> > pull_nstfout = 1<br>> > pull_ngroups = 1<br>> > pull_group0 = r_1-30<br>> > pull_group1 = r_31-60<br>> > pull_vec1 = 1 1 0<br>> > pull_init1 = 0.0<br>> > pull_rate1 = 0.05<br>> > pull_k1 = 30<br>> > pull_constr_tol = 1e-06<br>> > pull_pbcatom0 = 0<br>> > pull_pbcatom1 = 0<br>> > <br>> > Fabrício Bracht<br>> > <br>> > <br>> > Ragnarok sdf wrote:<br>> > > I am trying to learn how to use the pull code to separate a dimer. I<br>> > > have read gromacs 4 manual and a tutorial I found on CSC, but it<br>> > seems I<br>> > > still haven´t got the knack.<br>> > > My system is consisted of a dimer inserted into a membrane lipid<br>> > > bilayer. I have included the following lines into my mdp<br>> > parameter file.<br>> > ><br>> > <br>> > So the goal is to pull the dimer apart, within the plane of the bilayer?<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>> > <br>> > With a pull rate of 0, nothing is going to get pulled apart. With<br>> > umbrella<br>> > pulling and a pull rate of 0, the distance between the two groups is<br>> > going to be<br>> > restrained at its initial value, as I understand it.<br>> > <br>> > > pull_k1 = 1000<br>> > ><br>> > > Since I am trying to separate the two structures I thought about<br>> > using<br>> > > the DPPC membrane as a reference structure for the pull, since my<br>> > <br>> > With DPPC as the reference, then pulling would occur between the COM<br>> > of the<br>> > pulled group and the COM of the bilayer. If they lie at the same<br>> > place (i.e.,<br>> > protein dimer centered within the bilayer), I don't think this will<br>> > work.<br>> > <br>> > > attemps with the monomer as a reference struture went with nothing<br>> > > happening whatsoever. Is it correct to use such a long series of<br>> > > aminoacids as a pull reference, i.e., gromacs will understand<br>> > that tha<br>> > > pull should be in the center of mass, right? What does the manual<br>> > mean<br>> > <br>> > COM pulling should indeed be applied to the center of mass of<br>> > whatever you are<br>> > trying to pull on.<br>> > <br>> > If you're trying to separate a dimer, I would try setting<br>> > pull_group0 = Protein1<br>> > and pull_group1 = Protein2 (and apply a pull rate > 0). Just a<br>> > guess worth<br>> > trying; I'm still figuring my way through the pull code for a few<br>> > things, too :)<br>> > <br>> > -Justin<br>> > <br>> > > with "grompp normalizes the vector"? Is this how I should procede to<br>> > > separate my dimer?<br>> > > Thank you in advance<br>> > > Fabrício Bracht<br>> > ><br>> > ><br>> > <br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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