[gmx-users] low concentration simulation ?

Chris Neale chris.neale at utoronto.ca
Tue Jan 5 22:38:27 CET 2010

Mark already answered this:

--original message --

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?
Thank you

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