[gmx-users] Umbrella Sampling for a single molecule

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 25 17:24:29 CET 2011

Sai Pooja wrote:
> Hi,
> I am interested in carrying out umbrella sampling for a protein in 
> explicit solvent with the charmm forcefield. I want to impose a harmonic 
> potential in the dihedral space of only some specific atoms in the 
> protein molecule. I am having trouble figuring out a way to apply this 
> using gromacs. Can I get some help on this?


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.


> Thanks
> Pooja
> p.s. I have seen the tutorial on US by Justin but I am not sure if that 
> is applicable to a single molecule when the purpose is to obtain the 
> free-energy function associated with the transition in dihedral angles 
> of specific some atoms in a protein molecule
> -- 
> Quaerendo Invenietis-Seek and you shall discover.


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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