On Mar 7, 2013, at 2:59 AM, Justin Lemkul wrote:
On 3/6/13 8:57 PM, Vishwambhar Bhandare wrote:
dear gromacs user,
how i can do binding free energy calculation for RNA duplex in
gromacs?
any tutorial for the same??
Free energy calculations involving interactions between
macromolecules are typically done with umbrella sampling. A
tutorial is linked from gromacs.org, otherwise refer to the
literature for suggested methodology.
The challenge is likely to find a proper reaction coordinate and
assure that you sample sufficiently along it. You may end up wasting a
lot of computer time if you make a poor choice.
Erik
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