[gmx-developers] low concentration simulation ?

[Mark Abraham]

Chih-Ying Lin wrote:
>  
>  
> HI

This is not a question for the developers mailing list. I'll answer it 
on the users mailing list.

Mark

> 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.
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>  
> 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?
>  
> Thank you
> Lin
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