[gmx-users] Re: [gmx-developers] low concentration simulation ?

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 5 08:51:48 CET 2010

Chih-Ying Lin wrote:
> HI
> I am simulating the protein + ligand + water molecules system.
> In the experimental work, the concentration of ligand is pretty low, say 
> under 20 mM   (avearge 18 ligands attached on one protein)
> It will be a huge system to create a system with 20 mM and it will take 
> lot of simulation time.
> Instead, I create a 6nm x 6nm x 6nm simulation box and put one protein 
> molecule with 10 ligands.
> After 100 nano seconds, 10 ligands are attached on the protein.
> Then, for this one protein with 10 ligands attached  + water molecules 
> I will do the following steps =>
> 1. remove the water molecules
> 2. center the protein with 10 ligands attached in the 6nm x 6nm x 6nm 
> simulation box
> 3. put another 10 ligands around the protein with 10 ligand attached
> 4. solvate the system
> 5. add ions
> Are the above steps make sense to create a low concentration simulation?

Seems vaguely plausible. The problem with reproducing a bulk 
concentration of a minor species is that it was normally measured when 
the ratio of solvent volume to (e.g.) protein volume was extremely 
large, and a simulation can't afford that. For trying to reproduce 
experimental conditions with small volumes, you need to know about the 
protein/bulk-solvent "interfacial" concentration, which is hard to study 
experimentally. Traditionally, you guess something plausible and hope 
for the best... preferably a range of plausible choices and see what you 


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