Emanuel Peter wrote:
The standard procedure of H+ interchange and transition states can be done
through QM/MM.
Please give one reference according to the algorithms you have mentioned.
There are several cited at:
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
-Justin
Cheers.
>>> João M. Damas 06.09.11 15.19 Uhr >>>
As Justin said, constant protonation != constant pH.
Constant-pH MD does not simulate H+, but allows changes in protonation
states during the MD simulation. There are different algorithms
to accomplish that.
Cheers,
João
On Tue, Sep 6, 2011 at 2:04 PM, Emanuel Peter
<emanuel.pe...@chemie.uni-regensburg.de
<mailto:emanuel.pe...@chemie.uni-regensburg.de>> 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.
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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Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613
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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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