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

[Evelyne Deplazes]

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