[gmx-users] Re: Pull to separate dimer
fabracht1 at gmail.com
Sun Aug 23 01:53:54 CEST 2009
> 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.
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:
; 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
> 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
> 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
> trying to pull on.
> If you're trying to separate a dimer, I would try setting pull_group0 =
> 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 :)
> > with "grompp normalizes the vector"? Is this how I should procede to
> > separate my dimer?
> > Thank you in advance
> > Fabrício Bracht
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