[gmx-users] pH

Oliver Beckstein oliver at biop.ox.ac.uk
Tue Aug 12 22:02:01 CEST 2003


I think you wouldn't typically put xN protons and 10^-14/x N OH- in your
simulation box; if you do the math you'll see that with a N = few thousand
water molecules in your simulation you won't get many protons at
these pH... 

So what people do is calculate the protonation states of the titrable
sidechains in a static structure at a given pH and use these as input
for their MD simulations. In order to obtain titration curves the free
energy of ionisation of a sidechain has to be calculated. These are
electro static calculations in presence of a salt solution. Typically,
this means that the (linearised) Poisson-Boltzmann equation has to be
solved repeatedly, using your choice of DelPhi, UHB, APBS, ...

However, Jose Faraldo-Gómez, a colleague of mine, has written half a
thesis about this, which is online available at
http://sansom.biop.ox.ac.uk/josed/home.html (see especially Chapter
4). This uses UHBD and a couple of home grown scripts.

Alternatively you can look at WhatIf/DelPhi, and here I can recommend
Jens Nielsen's pages,
http://mccammon.ucsd.edu/~jnielsen/manuals/pKa.html and links from


On Tue, 12 Aug 2003, Osmany Guirola Cruz wrote:

>  Hi 
> Two questions.I have my system(for example a peptide in a box of water)
> How can I calculate the pH of the sysytem and 
> How can I do a simulation of this system whith a given pH.
> For example I want a simulation of the system whith pH=4 and another
> whith
> pH=9..  
> Thanks...

Oliver Beckstein * oliver at bioch.ox.ac.uk

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