Hello,
I am trying to simulate some protein system in mixed solvents like water+acetaldehyde in a box of volume (~1109.18 nm3) or box size (12.2 x 9.0 x 10.04).
How many number of acetaldehyde molecules are required to make 50mM concentration of acetaldehyde and do I have to replace water molecules accordingly? Also, how many number of ions has to be added to neutralize the system according to 50mM acetaldehyde concentration?
I'm not sure if this is the right way to do the calculation, but for that size box, you'd need 33.397 acetaldehyde molecules. If I were you, I'd probably just do 33. If there is no room to place them, then yes, you will likely have to replace waters. As for neutralizing the system, in GROMACS, you can use gmx genion -neutral to create a neutralized system automatically.
Thanks all for the answer.
@JD Tamucci: can you provide the calculation?
Also, do I need to just neutralize the system by counterions or add the similar concentrations of ions (i.e. 50mM) by Genion?
Hi, for the electrostatic algorithms to work properly, you have to neutralize the system, otherwise, drift in charge will blow your system.
Adding ions on top of that to make 50mM Salt solution is your choice whatever you want to replicate/prove.
The box size does not matter. 55.5 / 0.05 = 1110 / 1. (1110 water molecules / 1 acetaldehyde molecule.)
There might be a more accurate way to calculate it, but this is all I did. (see picture) It might be better to do it based on the water density or something, I'm really not sure.
As for the ions, some people just do neutralizing counterions. It probably depends how many counterions you'd really be adding. I'm not an expert here. I will say that gmx genion gives you the option to neutralize your system or to both neutralize AND set a certain ion concentration.
The final option would add all the ions necessary to meet your desired concentration and then add more counterions to neutralize the system.
Regardless, like Muhammad Ayaz Anway said, you need to neutralize the system.
@Muhammad Ayaz Anwar: Thank you! I will first try by neutralizing the system and later try with salt concentration.
@Martin Klvana: Thank you Dr. Klvana for the answer!
@JD Tamucci: Thank you Mr.Tamucci! I will try with your solution and then match with empirical data.
Hi Anurag,
Could you help me with the details of how to decide on the box size? I am simulating a protein composed of 50 aa and in mixed solvents at 0.1, 1 and 2M concentration.
Vidya Sundaram The box size should depend on your solute size and must satisfy periodic boundary condition. Usually, the distance from your solute to box edge should be at least 1nm (so that your solute will not see its images within the cutoff)
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