[gmx-users] umbrella sampling
jalemkul at vt.edu
Mon Jul 16 16:29:07 CEST 2012
On 7/16/12 10:25 AM, Giovani Mancini wrote:
> Dear Gromacs users,
> I just read the tutorial by Justin Lemkul about umbrella sampling simulations along z-axis. My question is whether we need cylindrical confinement of the molecule that is pulling away from a reference molecule.
> Thanks in advance
The tutorial is a very simple system designed to get users familiar with a basic
workflow. There are more elegant ways of doing umbrella sampling for more
complicated systems. Cylindrical restraints can be useful in some cases and are
discussed in the manual. Without knowing more about the system you're
considering, it's hard to provide specific advice.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users