[gmx-users] Re: gmx-users Digest, Vol 64, Issue 147

[Ragnarok sdf]

Hi  Justin.
 So for each window, I would turn pull_rate to zero in order to get a system
in equilibrium?
And then the lambda value would be equal to each of the sampling distances?
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?
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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