[gmx-users] Steered MD: Gromacs 4.0

[Justin A. Lemkul]

Matthew L. Danielson wrote:
> Hi,
> I am having some trouble using the COM pulling code (Gromacs 4.0). I 
> will try to describe the problem as best I can and hopefully someone 
> will be able to point me in the right direction!
> 
> Basically what I would like to do is pull a ligand (LIG) along a 
> specified path from the interior of a protein to the exterior (Steered 
> MD simulation). Using the following .mdp file I was able to pull the 
> ligand, but it did not travel along the path that I thought it would (ie 
> along the vector specified in pull_vec1).
> Pull section of my md.mdp file:
> 
> pull            = umbrella
> pull_geometry         = position
> pull_dim         = Y Y Y
> 
> pull_r1         = 1
> pull_r0         = 1.5
> pull_constr_tol        = 1e-06
> pull_start         = no
> pull_nstxout         = 10
> pull_nstfout         = 1
> pull_ngroups         = 1
> 
> pull_group0         = pull_weights0         =
> pull_pbcatom0         = 0
> pull_group1         = LIG pull_weights1         =
> pull_pbcatom1         = 0
> pull_vec1         = -31.07-15.37 9.89
> pull_init1         = 43.416 66.914 40.125
> pull_rate1         = 0.001
> pull_k1         = 500
> pull_kB1        =
> 
> 
> I specified pull_vec1 as the vector I would like to pull the ligand 
> along (ie -x,-y,+z).  Looking at the simulation in VMD the ligand 
> traveled in the (+x, +y, +z) direction.
> In this trial I specified pull_init1 as the point I would like the 
> spring to be attached to the ligand.
> 
> I have read the gromacs 4.0 manual and many of the posts online, but I 
> still cannot seem to figure out what values are required in the 
> parameter file. I know the following pieces of information, but I don't 
> know how/if they fit into the parameter file:
> 
> 1. The point where I would like the spring to be attached to the ligand

I don't think that can be specified.

> 2. The vector along which I would like the ligand to travel

That's pull_vec1.

> 3. The distance between a reference atom in the protein and the desired 
> spring attachment point on the ligand
> 

Again, the spring attachment isn't something you set, but the initial distance 
is something you can set with pull_init1 or pull_start.

> 
> Anyone have any ideas of what i am missing or doing wrong?  Or if I am 
> missing some fundamental concept here?
> 

Are your units appropriate?  Is your box really that large?  Gromacs specifies 
all distances in nm, not Angstrom.  It may also be worthwhile to upgrade to the 
latest version (4.0.7); there have been several fixes for overall stability of 
the code since version 4.0, some of them pertinent to the pull code.  See the 
revision history on the Gromacs site for this important information.

-Justin

> Thanks,
> Matt Danielson
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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