[gmx-users] Re: Pull to separate dimer
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,
> > 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.
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
In both methods checking the convergence of the re/constraint force is critical.
> > ; 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
> > >
> > >
> > ------------------------------------------------------------------------
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users