<br><br><div class="gmail_quote">Hi Justin.<br> So for each window, I would turn pull_rate to zero in order to get a system in equilibrium?<br>And then the lambda value would be equal to each of the sampling distances?<br>
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?<div>
<div></div><div class="h5"><br>Ps: Sorry for the re-sending, I forgot to edit my subject box.<br>
Fabrício Bracht<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><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>
> ; 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>
</blockquote></div><br>
</div></div></div><br>