[gmx-users] is it possible?

Justin Lemkul jalemkul at vt.edu
Mon Nov 12 17:25:34 CET 2012

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


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