On 11/12/12 10:29 AM, Albert wrote:
Hello:
Recently, in a released paper I found that some one claimed they've observed a
Asp is protonated and deprotonated from time to time during a micro second MD
simulation by Gromacs. I am still curious about such kind of observation. Does
anybody else observe a covalent bond can be broken in normal MD simulations?
A link to the paper would be helpful, otherwise the commentary is a bit vague.
In classical MD, no, bonds cannot break and form, but there are ways of changing
protonation states (titration MD, dual-topology approaches with virtual sites,
etc). Titration MD is in the works for Gromacs, but at present, is not possible.
-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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