[gmx-users] Deprotonation and charging of a non-protein in salt solution

Steven Kirk Steven.Kirk at htu.se
Wed Nov 2 04:07:04 CET 2005


I have a large (5nm diameter) particle of amorphous silica in my 
simulation box, generated using x2top and some OPLS-AA parameters and 
kind advice from David Spoel. The particle consists of only Si, O, and 
H, and all atoms show up in my topology as uncharged. All of the H atoms 
are hanging off Si-OH groups on the particle surface.

I now want to partially deprotonate the particle, to mimic the effect of 
pH in a TIP4P water solvent box with a known fixed number N of randomly 
inserted Na+ counterions present(inserted using genion), so that the 
particle acquires a negative charge and the simulation cell is 
electrically neutral.

My naive strategy looks like this:

1. Randomly select a number N of H atoms on the particle surface and 
remove them.
2. Set a charge of -1 on those surface O atoms which have been 
deprotonated (how?).
3. Let the whole cell contents relax (eventually, hopefully, to an 
particle surrounded by a stable electrical double layer)

Can anyone suggest an easy (preferably automated) procedure to generate 
such a (hopefully chemically consistent) configuration? What files would 
need to be edited and how? Even just one such possible configuration 
would be useful, but of course the ability to generate an ensemble of 
such randomly edited structures progammatically would be even more useful.

Many thanks in advance,
Steve Kirk

Dr. Steven R. Kirk          <Steven.Kirk at htu.se, S.R.Kirk at physics.org>
Dept. of Computer Science, TMD               http://taconet.webhop.org
Univ. of Trollhattan/Uddevalla   Ph: +46 520 475318 Fax:+46 520 475399
P.O. Box 957 Trollhattan 461 29 SWEDEN

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