It it better to evaluate ion adsorption energy for the each ion using Monte Carlo (MC) simulation, rather than MD. Add your answer

Thanks Ramin for you reply,

I am wondering if I can use GROMACS to do this kind of evaluation? Or you suggest other tool?

Thank you,

I do not think so the Gromacs can do it. Please have a look here,

http://www.tandfonline.com/doi/full/10.1080/08927022.2015.1010082

Thank you, It seems it is not designed for ion-protein interaction. Actually I want to compare the stability of different ions in binding site of a specific enzyme.

Dear Mohamad

You can do this study using Gromacs. You have to maintain your ions concentration in your water box and run the simulation. Prepare separate topology file manually for your ions and add in to your main topology file. You can prepare ion topology manually from previous literatures. Recently I'm working on such problems. If further clarification needed you can contact me.

Thanks