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.
http://mmtsb.org/workshops/mmtsb-ctbp_workshop_2009/Tutorials/CPHMD/cphmd_tutorial.html)
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
constant pH.
-Justin
monkey.
>>> João M. Damas 06.09.11 14.22 Uhr >>>
That is not considered constant-pH MD.
Follow Justin's suggestion.
Cheers,
João
On Tue, Sep 6, 2011 at 12:47 PM, Emanuel Peter
<emanuel.pe...@chemie.uni-regensburg.de
<mailto:emanuel.pe...@chemie.uni-regensburg.de>> wrote:
Look for the pKa-constants of each part of your system (e.g. each
amino-acid).
Then you can check each protonation state and change it according to
your
application in the force-field.
Emanuel
>>> 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
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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