[gmx-users] minimisation with protonated residues

Justin Lemkul jalemkul at vt.edu
Thu Sep 6 17:30:23 CEST 2012

On 9/6/12 11:27 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Ah okey.
> Thank you for the helpful answer.
> In some cases it can also be that the phosphate is not protonated at all.
> Does gromacs also recognize that a proton at this position would make no
> sense and remove it from the structure?

No.  Gromacs does what you tell it.  If your topology has a proton, the 
simulation is carried out as such.



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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