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 email@example.com 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
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.
cp run* *pot c1.topo md_temp.inp get_pot_mean_force T_300 ; cd T_300
# PMF Input script template # (1) Initialisation units real atom_style full boundary p p p pair_style hybrid/overlay lj/charmm/coul/long 10.0 12.0 buck/coul/long 12.0 morse 10.0 bond_style harmonic angle_style harmonic dihedral_style charmm kspace_style pppm 0.0001 # (2) Define atoms read_data c1.topo group molecule molecule 1 group substrate molecule 2 group bottom molecule 3 # (3) Settings # freeze bottom layer of substrate to prevent it from drifting fix 2 bottom setforce 0 0 0 include new_defpot.pot include best_all.pot neighbor 2.0 bin neigh_modify delay 0 timestep 1.0 # (4) NVT Dynamics fix temp1 molecule nvt temp _TEMP_ _TEMP_ 100 fix temp2 substrate nvt temp _TEMP_ _TEMP_ 100 velocity all create _TEMP_ 293288 fix PMF molecule recenter NULL _Y_ NULL compute temp_molecule molecule temp compute yforce molecule group/group substrate kspace yes thermo_style custom time c_yforce etotal pe c_temp_molecule temp ke evdwl press enthalpy thermo_modify flush yes thermo 50 dump xyz all xyz 100000000 mol_sub.xyz dump_modify xyz element C C H C N K Cl dump coord all dcd 5000 trajectory.dcd restart _NSTEPS_ TCB_PMF.restart run _NSTEPS_
gnuplot gnuplot> load "pot_mean_force.gnu"
cd REF_300 cp ../get_pot_mean_force . ./get_pot_mean_force gnuplot gnuplot > plot "pot_mean_force" w lp