[gmx-users] low concentration simulation ?

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 5 22:37:41 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?

Your procedure sounds more like a titration with increasing concentration, 
rather than modeling a low concentration system.  If you say that you have 20 mM 
of ligand, which corresponds to 18 ligands attached to one protein, why not just 
put 18 molecules in your unit cell with one protein?  You may never be able to 
achieve the actual concentration, but you can certainly model the mole ratio.

The other concern would be - if a system initially had 20 ligands (or 18, 
whatever), can you guarantee that the ligands will interact the same way as if 
you add ten at a time?  Will they aggregate?  Will they inherently bind the 
protein in the same way, or will it be different?


> Thank you
> Lin


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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