[gmx-users] Re: Pull to separate dimer

Berk Hess gmx3 at hotmail.com
Mon Aug 24 11:52:12 CEST 2009 



> Date: Sat, 22 Aug 2009 20:01:19 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: Pull to separate dimer
> 
> 
> 
> 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
> 

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

> >  ; 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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