Antw: Re: [gmx-users] constant PH simulations
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 6 15:10:38 CEST 2011
Emanuel Peter wrote:
> Could you just tell me smth. !
> No forcefield on whole earth is able to reproduce the pH realistically
> by H+.
> You just can apply pH of your system through the protonation states
> of each part in your system.
Constant protonation state and constant pH are different. Gromacs does not have
the capability of doing constant pH simulations since such algorithms (i.e.
are not implemented. One can make an argument that comparing protonation states
can be useful (I've done it), but you cannot equate constant protonation with
> >>> João M. Damas 06.09.11 14.22 Uhr >>>
> That is not considered constant-pH MD.
> Follow Justin's suggestion.
> On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter
> <Emanuel.Peter at chemie.uni-regensburg.de
> <mailto:Emanuel.Peter at chemie.uni-regensburg.de>> wrote:
> Look for the pKa-constants of each part of your system (e.g. each
> Then you can check each protonation state and change it according to
> application in the force-field.
> >>> fancy2012 __ 06.09.11 13.01 Uhr >>>
> Dear gmx users,
> Are there some tutorials on constant PH simulations using gromacs?
> How should I state my work? Right now I have no idea on it.
> _Best wishes,_
> _Qinghua Liao_
> _Ph.D student of Tianjin University, China_
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> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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