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exercises:2017_ethz_mmm:md_ala [2017/02/22 10:01] (current)
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 +====== Molecular Dynamics simulation of a small molecule====== ​
 +
 +
 +
 +<note important>​ **REMEMBER: this is the command to load the  module for the cp2k program:**
 +
 +<code bash>
 +you@eulerX ~$ module load new cp2k
 +</​code>​
 +
 +**and to submit the job:**
 +
 +<code bash>
 +you@eulerX ~$ bsub < jobname
 +</​code> ​
 +</​note> ​
 +
 +
 +
 +
 +Download the 4.1 exercise into your $HOME folder and unzip it:
 +<code bash>
 +you@eulerX ~$ wget http://​www.cp2k.org/​_media/​exercises:​2016_ethz_mmm:​exercise_4.1.zip
 +you@eulerX ~$ unzip exercises:​2016_ethz_mmm:​exercise_4.1.zip
 +you@eulerX ~$ cd exercise_4.1
 +</​code>​
 +
 +<note tip>
 +All files of this exercise (**all inputs are commented**) can be also downloaded from the wiki: {{exercise_4.1.zip|exercise_4.1.zip}}
 +</​note>​
 +
 +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:
 +
 +
 +<code - md_part.inp.nve>​
 +&​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
 +</​code>​
 +
 +<note tip>
 +To get more information,​ please visit **cp2k reference manual**, section **Molecular Dynamics**:
 +http://​manual.cp2k.org/​trunk/​CP2K_INPUT/​MOTION/​MD.html
 +</​note>​
 +
 +  * Perform a constant energy simulation, 100000 time steps, with a time step of 1 fs. Use 100 K as an initial temperature!
 +
 +<code bash>
 +you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.nve -o out.nve
 +</​code>​
 +<note tip>
 +Assignments:​
 +  - We are performing MD at a constant energy, but why we still have to define the temperature?​
 +</​note>​
 +
 +  * Make four copies of the previous input file (say inp.nve_0.1,​ inp.nve_2.0,​ inp.nve_3.0,​ inp.nve_4.0),​ in each input file modify the **time step** (use 0.1, 2, 3, 4 fs respectively) ​ and the **name** of the project. ​
 +  * Perform the simulations with all these input files: ​
 +<code bash>
 +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
 +</​code>​
 +  * Have a look at the corresponding *.ener files (we suggest you to use gnuplot).
 +<note tip>
 +Assignments:​
 +  - Do you see the energy conservation?​ Give comments on your observations.
 +  - Analyse the behavior of potential and kinetic energy, and the temperature.
 +</​note>​
 +
 +<note important>​
 +Hint (plotting with gnuplot).
 +
 +To plot the Kinetic energy:
 +<code bash>
 +gnuplot> plot "​nve_md-1.ener"​ u 1:3 w l t "​Kinetic Energy"​
 +</​code>​
 +To plot the Potential energy:
 +<code bash>
 +gnuplot> plot "​nve_md-1.ener"​ u 1:5 w l t "​Potential Energy"​
 +</​code>​
 +To plot the Temperature:​
 +<code bash>
 +gnuplot> plot "​nve_md-1.ener"​ u 1:4 w l t "​Temperature"​
 +</​code>​
 +
 +
 +</​note>​
 +
 +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. ​
 +
 +<note important>​
 +Concerning temperature control, in these exercises we will use the NOSE-HOOVER chains method. This has been briefly described in the lecture, and is presented in [[doi>​10.1063/​1.463940|this paper]] by Glenn Martyna (1992).
 +</​note>​
 +
 +In cp2k input files you should again have a look at the following section:
 +<code - md_part.inp.300>​
 +  &​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
 +</​code>​
 +
 +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: 
 +<code bash>
 +you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.100 -o out.100
 +</​code>​
 +  * Then, perform another simulation, using the restart file from the previous simulation: **inp.300**. But first you have to edit it exactly like in the previous case, except of the temperature which you set as ** 300 K** instead of 100 K
 +<code bash>
 +you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.300 -o out.300
 +</​code>​
 +
 +Now you have the following outputs to study with vmd:
 +<​code>​
 +nve_md-pos-1.pdb
 +md.100-pos-1.pdb
 +md.300-pos-1.pdb
 +</​code>​
 +
 +  * Open (for example) nve_md-pos-1.pdb with VMD:
 +
 +<code bash>
 +vmd nve_md-pos-1.pdb ​
 +</​code>​
 +
 +  * Open Tk Console (Extensions menu > Tk console). And to define the two dihedrals (**PHI** and **PSI**) from there, you can enter:
 +
 +<code tcl>
 +vmd> source "​dihedrals.vmd"​
 +</​code>​
 +
 +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.
 +
 +  * Now using "​Labels"​ menu, plot the graph of two dihedral angles:
 +  - Go to Graphics > Labels
 +  - In the drop-down list chose Dihedrals
 +  - Chose both dihedrals in the list
 +  - Go to the "​Graph"​ section
 +  - Press on the "​Graph..."​ button
 +  - (Optional) save these graps in a text file (File > Export to ASCII matrix...)
 +
 +<note tip>
 +Assignments:​
 +  - Which differences do you notice between the nve, the 100 K and the 300 K case? Can you explain them?
 +  - Explore how the behaviour of the system changes with increasing of the temperature. Use inp.300 and change it in order to perform the simulations at 500K, 700K, 1000K. Comment on your observations. ​
 +</​note>​
 +
  
exercises/2017_ethz_mmm/md_ala.txt ยท Last modified: 2017/02/22 10:01 (external edit)