[gmx-users] Pull to separate dimer

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 22 05:03:07 CEST 2009

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 :)


> 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


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