I would like to use gromacs to simulate a protein in presence of high concentration of polymers. The issue I am facing is with the number of polymer I should add. Earlier when I worked with spherical molecules, I could easily use their van der Waals volume and simulation box volume to determine number of molecules required for a certain value of crowder volume fraction. However, for a flexible system like a polymer it is becoming more difficult.
How do I determine the number of polymer (e.g. PEG) required for a specific value of the volume fraction of the polymer using gromacs? Any help would be much appreciated.
For example: if I start with a protein of mol. wt. of 14 kDalton (mass of one protein approximately is 2.32 x 10^-20 g) and 8000 TIP3P water molecules (total mass: 8000 x 18 dalton / (6.022 x 10^23) = 2.4 x 10^-19 g), the total mass of the solution is ~ 27 x 10^-20 g.
If I want to add 20% (w/w) PEG-200 (mol. wt. 200 dalton or 3.2 x 10^-22 g per molecule), then 20% mass of the entire solution = 0.2 *27x10^-20 = 5.4 x 10^-20 g. So, the number of PEG required will be = 5.4 x 10^-20/( 3.2 x 10^-22) = 163 (approximately)
if we divide the mass by the density we will get volume, and as the mass density of PEG, protein and water are nearly the same (approximation), we can use the same number for 20% volume fraction as well 20% mass fraction.
This is what I have understood from what you have said. Please correct me if I am wrong. Thanks