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?
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints
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.
-Justin
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
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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