[gmx-users] pH

Marc Baaden baaden at smplinux.de
Wed Aug 13 09:30:01 CEST 2003


we did some work on the influence of acidity. Unfortunately it does
not go as far as using a real pH, but we rather did test extreme cases
where you have explicit acid molecules present which are either
dissociated, associated or partly dissociated by protonating part
of the system.
In our case it did make sense because the real concentrations in
the system we were looking at (nuclear waste recycling) were *very*
But one can always try it.

If you are interested, have a look at

     M. Baaden, F. Berny and G. Wipff; "The chloroform / TBP / aqueous
     nitric acid interfacial system: a molecular dynamics
     investigation.", J. Mol. Liq., 90, 2001, 1-9.

     M. Baaden, M. Burgard, and G. Wipff; "TBP at the water - oil
     interface: the effect of TBP concentration and water acidity
     investigated by molecular dynamics simulations", J. Phys. Chem.
     B, 105, 2001, 11131-11141

For a protein with ionizable sidechains it would however in any case
be necessary to do a pka calculation in addition and adapt the protonation


>>> "Xavier Periole" said:
 >> The pH involves the entities OH- and H+(H3O+). Do you have any in
 >> your system ? Probably not !! They do not exist in any Molecular 
 >> Dynamics force field I know. I don't know any way to do explicit 
 >> solvent simulations with a control of pH. 
 >> I assume that the pH can be introduce when the solvent is introduced 
 >> explicitly. But I don't know either any explicit solvent where you can 
 >> actually modify your pH. Does any one ??? 
 >> XAvier
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Marc Baaden

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217

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