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For this job we will use the cluster HYPATIA available at Empa. There we have access to parallel facilities with reserved nodes for the lecture. How to connect to HYPATIA:

Dear Student,

In order to be able to run simulations at high priority, today we will work on the Empa Cluster. We have created a personal account for you. Since the cluster is behind a firewall, we must connect to a gate machine (jumphost) to be allowed to access to the cluster.

Here the instructions to connect.

1) Decide a username for hypatia (it will be one between mmmstud01 and mmmstud25 ) 2) connect to the jumphost with the username (same for all) mmmstud

ssh -X mmmstud@jump1.empa.ch Password: will be communicated in the class

3) Connect to hypatia: ssh -X mmmstud02@hypatia (replace “02” by your number) password: same as username

4) you are in!

[you@hypatia ~]$ mmm-init
[you@hypatia ~]$ cd /mnt/scratch/YOURUSER/
[you@hypatia ~]$ cp -r /mnt/scratch/psd/exercise_12 .
[you@hypatia ~]$ cd exercise_12

Reproducing a PMF calculation for adsorption of an organic molecule on KCl

We will today refer to the paper available at 10.1021/acs.jpcc.5b12028 about the entropic effects of adsorption of pretty large molecules on KCl. We will use the software LAMMPS for performing a series of MD simulations at fixed molecular height above the surface. Then we will use integration of the average force between the molecule and the substrate, along the adsorption path, to extract the free energy difference between two configurations: the “very far” configuration and a configuration along the path.

After you copied the exercise_12 directory and entered it, look at the l1.xyz file (by editing or vmd) and understand the geometry of the system: which range of distances should you consider for MD runs?
Create a directory T_300 and copy into it the following files run* *pot c1.topo