you@eulerX ~$ module load courses mmm vmd
you@eulerX ~$ mmm-init
you@eulerX ~$ module load new cp2k
and to submit the job:
you@eulerX ~$ bsub < jobname
Download the 4.1 exercise into your $HOME folder and unzip it:
you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_4.1.zip you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_4.1.zip you@eulerX ~$ cd exercise_4.1
You will start from a configuration already computed in the second lecture (inp.a.pdb) which is included in the repository of this exercise as well. Update the following part of the file inp.nve for the first simulation:
&MD ! This section defines the whole set of parameters needed perform an MD run. ???????? ??? ! Please specify the appropriete ensemble for you MD simulation ????? ?????? ! Please specify the number of MD steps to perform ???????? ???? ??? ! Please specify the length of an integration step ??????????? ????? ! Please specify the initial temperature &END MD
you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve -o out.nve
you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve_0.1 -o out.nve_0.1 you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve_2.0 -o out.nve_2.0 you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve_3.0 -o out.nve_3.0 you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve_4.0 -o out.nve_4.0
To plot the Kinetic energy:
gnuplot> plot "nve_md-1.ener" u 1:3 w l t "Kinetic Energy"
To plot the Potential energy:
gnuplot> plot "nve_md-1.ener" u 1:5 w l t "Potential Energy"
To plot the Temperature:
gnuplot> plot "nve_md-1.ener" u 1:4 w l t "Temperature"
Now you will perform a constant Temperature simulations, where the system is in contact with a thermostat, and the conserved quantity includes the thermostat degrees of freedom.
In cp2k input files you should again have a look at the following section:
&MD ! This section defines the whole set of parameters needed perform an MD run. ???????? ??? ! Please specify the appropriete ensemble for you MD simulation ????? ?????? ! Please specify the number of MD steps to perform ???????? ??? ! Please specify the length of an integration step ??????????? ??? ! Please specify the temperature of the simulation &?????????? ! Please specify a thermostat section here &???? ! Please put here a section which specfies Nose-Hoover thermostat chain TIMECON 50 ! Timeconstant of the thermostat chain LENGTH 3 ! Length of the Nose-Hoover chain YOSHIDA 3 ! Order of the yoshida integretor used for the thermostat &??? &??? &END MD
Edit the inp.100 file (Put there: NVT ensemble, 100000 steps of simulation, 100 K, Nose-Hoover thermostat and 1.0 fs of timestep). The first simulation is done at 100 K:
you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.100 -o out.100
you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.300 -o out.300
Now you have the following outputs to study with vmd:
nve_md-pos-1.pdb md.100-pos-1.pdb md.300-pos-1.pdb
vmd nve_md-pos-1.pdb
vmd> source "dihedrals.vmd"
You can also pick from the extensions the “RMSD trajectory tool” and use it to align the molecule along the trajectory (Extensions>Analysis>RMSC Trajectory Tool). Replace the word “protein” with “all” in the selection, and then use “align”. You will see that now the molecule is well aligned along the path.