[gmx-users] is it possible?

[Justin Lemkul]

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

-- 
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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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