[gmx-users] Umbrella sampling along a dihedral angle

Nash, Anthony a.nash at ucl.ac.uk
Sat Dec 27 00:11:10 CET 2014

Dear Gromacs community,

Using enforced rotation potentials I have generated a really smooth rotation of my ligand the catalytic binding domain of my protein. I then put together a simple perl script to calculate the dihedral angle of four particular atoms at each time step using g_angle. Taking a 6 degree interval (for a total of 60 windows to span the 360 degree rotation) I modified the topology with a [ dihedral_restraint ] with the respective dihedral angle for that particular configuation. I plan on then running each window for 10 ns to begin with (according to the PMF profile I can add more time). It is from this point where I am a little stuck.

I have gone through a number of posts going back to 2011 with regards to using umbrella sampling along a dihedral angle reaction coordinate. The precise post was from Justin:

"You'll have to build various configurations that correspond to different dihedral angles (which form the sampling windows), then restrain them.

The energy attributed to the restraints is then stored in the .edr file. From these energies, you should be able to construct the energy curve over the sampling windows. There are examples of this in the literature, so I suspect you should be able to find some demonstrations of how it's applied."

I was wondering whether gromacs now support this procedure natively? I noticed g_wham has an option -cycl for dihedrals but I am still not sure how this fits in with the traditional gromacs means of generating pull force output as I have only been using distance based rather than angular based umbrella sampling. 

Many thanks to any insight.

More information about the gromacs.org_gmx-users mailing list