[gmx-users] removing rotational and translational motion (holonomic contraint)

[Tsjerk Wassenaar]

Hi Evelyn,

You can download version 3.3.1 with the rotational constraints from
http://nmr.chem.uu.nl/~tsjerk/gromacs-3.3.1-rtc.tgz
That is the original implementation of Amadei, with a few minor
modifications to deal with jumps of molecules over boundaries.

Hope it helps,

Tsjerk

On Tue, Mar 12, 2013 at 2:38 AM, Evelyne Deplazes <e.deplazes at uq.edu.au> wrote:
> Hi guys
>
> I am running a set of umbrella sampling simulations using gromacs 333 and the "pull" code. The idea is to apply an umbrella potential to restrain the distance between a protein and a ligand in the x direction. Unfortunately, the rotational and translational movement of the protein during the MD run interferes with my restraining of the protein-ligand distance. I am therefore interested in applying a rotational and translational constraint to my protein.
>
> Amadei et al described a solution to this problem in their J Chem Phys paper (see below). The problem was also discussed in the following gromacs post:
>
> http://lists.gromacs.org/pipermail/gmx-users/2003-May/005591.html
>
> Extract from the post:
>
> "For a simulation in solvent it is less trivial but feasible as was shown
> by Andrea Amadei and coworkers. They devised a method which constrains
> roto-translational movements of a solute, described in J. Chem. Phys.
> 112(1) pp. 9-23.
>
> They've implemented the method in Gromacs and a patch can be obtained
> from Danilo Roccatano ( roccata at caspur dot it ) from that group. We
> will be trying to implement things properly into Gromacs in the near
> future here in Groningen, but it has to wait a bit. If it's done we'll
> put it forward for a future release."
>
> There is another post in 2006 that refers to a patch for removing roto-translational motion but the link no longer works.
>
> http://gromacs.5086.n6.nabble.com/Protein-rotation-in-triclinic-waterbox-td4413734.htm<http://gromacs.5086.n6.nabble.com/Protein-rotation-in-triclinic-waterbox-td4413734.html>
>
> Finally, there is a more recent post (2012) stating it has been implemented in version 4.5.1 and 4.5.3 but not released.
>
> http://gromacs.5086.n6.nabble.com/roto-translational-constraints-td4390750.html
>
> Has this feature been implemented in the official gromacs version? Can I obtain the patch and use it with gromacs 333?
>
> Thanks a lot
> Evelyne
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada