[gmx-users] Re: Re: Pull to separate dimer
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 23 03:00:19 CEST 2009
Ragnarok sdf wrote:
>
>
> Hi Justin.
> So for each window, I would turn pull_rate to zero in order to get a
> system in equilibrium?
Yes, I believe that is correct. The umbrella potential is used to restrain the
configuration within a given window.
> And then the lambda value would be equal to each of the sampling distances?
I do not understand how the free energy code is related to the pull code. I
have been doing my data collection simply with independent umbrella sampling
simulations.
> 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?
>
Search the literature for relevant values; somewhere between 0.01 - 0.05 nm/ps
for a pull rate seems to be the consensus. I have seen wide ranges for the
force constant; I don't know what the consensus is there, if there is one.
-Justin
> Ps: Sorry for the re-sending, I forgot to edit my subject box.
> Fabrício Bracht
>
>
>
> 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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