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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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