[gmx-users] RE: Re: Pull to separate dimer
Ragnarok sdf
fabracht1 at gmail.com
Mon Aug 24 14:06:21 CEST 2009
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?
Fabrício Bracht
>
>
> I personally prefer using a constraint instead of an umbrella potential.
> This avoids choosing a force constant and avoid the WHAM procedure.
>
> You can also start the re/constrained simulation from the last
> configuration
> at the previous distance. But this is not convenient if you want to run
> multiple
> simulations simultaneously.
> In both methods checking the convergence of the re/constraint force is
> critical.
>
> Berk
> >
> > Ragnarok sdf wrote:
> > > 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.
> > >
> >
> > The pull rate is how fast the applied force moves; pull_k1 is the force
> constant
> > of the spring doing the pulling.
> >
> > > 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,
> >
> > Yes.
> >
> > > 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:
> >
> > I've yet to find a good tutorial for this purpose. If anyone else knows
> of one,
> > I'd be curious. I've been doing some pulling lately to calculate PMF for
> > various ligand-binding events. The way I think things need to go is:
> >
> > 1. Generate a trajectory of configurations along the reaction coordinate.
> > 2. Use different configurations as the starting points for independent
> > simulations in each sampling window.
> > 3. Use umbrella sampling to restrain these configurations within the
> windows.
> > 4. Calculate PMF from these simulations.
> >
> > If anyone else has a better or more complete explanation, I'd like to see
> it,
> > too; the documentation on the subject is a bit thin.
> >
> > -Justin
> >
>
> > > ; 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
> > >
> > > Fabrício Bracht
> > >
> > >
> > > 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 (i.e.,
> > > 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 are
> > > trying to pull on.
> > >
> > > If you're trying to separate a dimer, I would try setting
> > > pull_group0 = Protein1
> > > 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 :)
> > >
> > > -Justin
> > >
> > > > 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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> > --
> > ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
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