[gmx-users] umbrella sampling

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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