4.5. Example: Li+, Na+, and Cs+ in (C6H6)6

Tip

The sample input and output files can be found in testfiles/rigidmol/2-mben.

The systems here are benzene-solvated cations: \(\mathrm{Li}^{+}\), \(\mathrm{Na}^{+}\) and \(\mathrm{Cs}^{+}\) in \(\left(\mathrm{C}_6\mathrm{H}_6\right)_{6}\). The parameter files are misc/charmm36/li.xyz, misc/charmm36/na.xyz, misc/charmm36/cs.xyz, and misc/charmm36/c6h6.xyz.

Let’s first consider \(\mathrm{Li}^{+}\).

Step 1: Prepare an input file named li-ben6.inp with the following content:

li-ben.inp

li-ben.cluster # cluster file name
20             # population size
20             # maximal generations
3              # scout limit
10.00000000    # amplitude
li-ben         # save optimized configuration
30             # number of LMs to be saved

Step 2: Copy misc/charmm36/li.xyz and misc/charmm36/c6h6.xyz to the current path. Then prepare the cluster file named li-ben.cluster with the following content:

li-ben.cluster

2
c6h6.xyz   6
li.xyz     1
* 10.0000

Step 3: Run the global optimization:

$ rigidmol li-ben.inp > li-ben.out

After a few seconds, You will find the global minimum in li-ben-OPT.xyz and local minima in li-ben-LM.

For \(\mathrm{Na}^{+}\) and \(\mathrm{Cs}^{+}\), the global optimization procedure is similar. Below, the global minima are visualized (li-ben/0.xyz, na-ben/0.xyz, and cs-ben/0.xyz).