CHM 579 LAB 4(A): HYDRATED IONS

Solvation of ions and water structure around them is a big controversy. The goal of this lab is to learn how to do simple simulations of ions and salt solutions in GROMACS.

You may find useful information the GROMACS manual:

You may also need the GROMACS tutorials:

http://www.gromacs.org/Documentation/Tutorials

Scholar’s User Guide:

https://www.rcac.purdue.edu/compute/scholar/guide/

Lab Procedure:

These instructions assume that you have a working knowledge of GROMACS. The procedure steps are denoted with lowercase letters.

Step 1. SINGLE IONS

Perform a Molecular Dynamics simulation at 300 K under the isothermal-isobaric ensemble (NPT) of a system having a single solvated Cl- ion and other simulation for a single solvated Na+ ion.

a. Make a .gro file containing just 1 ion using arbitrary coordinates.

b. Use the editconf and genbox commands to solvate it. Use the box size corresponding to 216 water molecules (You may refer to previous assignments).

c. Do minimizations using the steep algorithm, then dynamics in NVT, and then NPT – similarly to what you did in previous assignments. However, use PME (Particle-Mesh Ewald sums) for the long range Coulombic interactions.

d. Run the MD simulation. Make sure to add "energygrps = Na SOL" in the .mdp file. This will allow you to analyze the interaction energies later on using g_energy script.

(A) Energy and dynamical properties of the single ions

1. Calculate the average potential energy of the whole system, discriminating between all the components. This can be done with g_energy command.

2. Calculate the average interaction energy of the ion with the solvent, discriminating all the energy component s. Again, use

g_energy for this.

3. Calculate the pair distribution functions for the ion-oxygen and ion-hydrogen.

4. Calculate the average diffusion coefficient of the ion.

Step 2. SEVERAL IONS

Perform a Molecular Dynamics simulation of a solution having 6 Na+ and 6 Cl-.

e. Use the output .gro file from one of the MD simulations containing a single ion and use the genion command to add more ions.

f. Repeat minimization, equilibration, and MD, similarly to steps c. and d. in Step 1.

(B) Energy and dynamical properties of several ions

5. Calculate the average potential energy of the whole system, discriminating between all the components.

6. Calculate the average interaction energy of the ion with the solvent, discriminating between all the components.

7. Calculate the average interaction energies between ions.

8. Calculate the pair distribution functions for the ion-oxygen and ion-hydrogen.

9. Calculate the pair distribution functions for ion-ion.

10. Calculate the diffusion coefficient of the ions.

(C) DISCUSION QUESTIONS

Read the paper by Jungwirth and Tobias (Chem. Rev. 2006, 106, 1259-1281). Then, answer the following questions:

11. Why do you have to use Ewald summations for treatment of the long-range electrostatic interactions in this lab?

12. How would you change the force field employed in this lab to obtain more accurate results?

Summarize and discuss the data obtained from simulations in parts A and B, and then answer these questions:

13. Compare water structure around positive and negative ions.

14. Does the water structure change when several ions are present simultaneously?

15. Do the ion diffusion coefficients change when several ions are present in the solution?

16. What is the relative importance of different potential energy components in simulations with one and several ions?