<div class="gmail_quote"><div>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?<br>
Fabrício Bracht <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><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>
> 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>
> > ; 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>
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><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]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
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</blockquote></div><br>