Hi everyone!!
While performing the MD simulations on proteins and studying their unfolding by Guanidium, How should one determine the guanidium concentration with regard to the number of molecules of guanidium added? I mean if i need a 4M gdm solution how many guanidium molecules must be used.The mole weight of my protein tetramer is 110Kda and monomer 27.5 Kda.Please help.
Assuming you have (100A)3 box
(100A)3*4mol/L=(100A)3*4*6.02*1023/10-3m3=(100A)3*4*6.02*1023/(10-3*1030A3)=2408
Just please mind that in NPT ensemble, your box might shrink during pressure equilibration. Therefore, always check your actual box volume after a period of equilibration to calculate the concentration properly.
If you don't understand my answer, you should not begin your research. That's the most basic knowledge.
volume * solute density = the amount of solute
1mol = 6.0223 molecules
1L = 10-3m3 = 10-3 * 1030 Angstrom3
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