Actually, i want to check effect of chloroform on my enzyme,so i am going for MD simulation with chloroform.But problem is that, i dont know how to calculate number of molecules in 50% v/v conc. ??
so please help me !
Use Avogadro's number for gram moles of molecules and the volume need to be changed to gram scale using density. Can you go through and handle rest!
Apart from Our discussion:
Lets calculate the number of molecules in a box of 10 x 10 x 10 = 1000 nm3.
Density of Chloroform = 1.49 g/cm3 = 1.49 g/1024 nm3
So, In a box of 1000 nm3, the chlorofrm = (1.49 x 1000)/1024 gram of chloroform.
*Change the gram into Moles. (divide by MM)
* X Moles = X * 6.022 * 1023 molecules of Chloroform.
So, you will come to know the number of molecules of Chloroform that can accommodate in a cubic box of 1000 nm3. You can calculate the same for WATER.
But remember, in practical, you will not get the same number. You can assume that X number of Chloroform molecules can be filled and Y number of water molecules in 1000 nm3 box. But Here we'ere ignoring the space occupied by Protein. So, while doing MD simulation, first solvate the system and check the number of molecules of water that can be added in the box. Accordingly you can Calculate the no. of molecules of Urea by analyzing the ratio X/Y=New X/ New Y.
For 50% Chloroform by Volume: Follow insert-molecules, -nmol New X/2.
Then Solvate with water. It will give you accurate conc. of Chloroform.
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