<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;">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. </blockquote>
<div>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, 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:<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></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<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 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 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 umbrella<br>
pulling and a pull rate of 0, the distance between the two groups is 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 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 of the<br>
pulled group and the COM of the bilayer. If they lie at the same place (i.e.,<br>
protein dimer centered within the bilayer), I don't think this will 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 that tha<br>
> pull should be in the center of mass, right? What does the manual mean<br>
<br>
COM pulling should indeed be applied to the center of mass of whatever you are<br>
trying to pull on.<br>
<br>
If you're trying to separate a dimer, I would try setting pull_group0 = Protein1<br>
and pull_group1 = Protein2 (and apply a pull rate > 0). Just a guess worth<br>
trying; I'm still figuring my way through the pull code for a few 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>
</blockquote></div><br>