exercises:2015_ethz_mmm:md_ala
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionLast revisionBoth sides next revision | ||
exercises:2015_ethz_mmm:md_ala [2015/03/09 15:40] – yakutovich | exercises:2015_ethz_mmm:md_ala [2015/03/13 15:24] – dpasserone | ||
---|---|---|---|
Line 3: | Line 3: | ||
<note warning> | <note warning> | ||
TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | TO USE THE FUNCTION LIBRARY (VERSION UP TO DATE) IN THE INTERACTIVE SHELL: | ||
- | you@eulerX ~$ module load courses mmm vmd ; mmm-init | + | |
+ | you@eulerX ~$ module load courses mmm vmd | ||
+ | |||
+ | you@eulerX ~$ mmm-init | ||
</ | </ | ||
Line 21: | Line 24: | ||
- | <note tip> | ||
- | 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> | ||
- | </ | ||
Line 34: | Line 34: | ||
<note tip> | <note tip> | ||
- | All files of this exercise (**input and scripts are all commented**) can be also downloaded from the wiki: {{exercise_4.1.zip|exercise_4.1.zip}}</ | + | All files of this exercise (**all |
+ | </ | ||
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. | 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. | ||
- | Use the file **inp.nve** for the first simulation, which is a constant energy simulation. | + | Update the following part of the file **inp.nve** for the first simulation: |
+ | |||
<code - md_part.inp.nve> | <code - md_part.inp.nve> | ||
& | & | ||
- | | + | |
- | | + | |
- | | + | |
- | | + | |
&END MD | &END MD | ||
- | |||
</ | </ | ||
- | | + | <note tip> |
+ | To get more information, | ||
+ | http:// | ||
+ | </ | ||
+ | |||
+ | | ||
<code bash> | <code bash> | ||
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 -o out.nve | ||
</ | </ | ||
- | - Using a different input file, modify the time step and the name of the project. Do it for 0.1, 2, 3, 4 fs. | + | <note tip> |
- | - Access the corresponding *.ener files. How is the energy conservation? | + | Assignments: |
- | <note important> | + | - We are performing MD at a constant |
+ | </ | ||
- | * Perform | + | |
- | The first simulation is done at 100 K: | + | |
+ | <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 | ||
+ | </ | ||
+ | * Have a look at the corresponding *.ener files (we suggest you to use gnuplot). | ||
+ | <note tip> | ||
+ | Assignments | ||
+ | - Do you see the energy conservation? | ||
+ | - Analyse the behavior of potential and kinetic energy, and the temperature. | ||
+ | </ | ||
+ | |||
+ | <note important> | ||
+ | Hint (plotting with gnuplot). | ||
+ | |||
+ | To plot the Kinetic energy: | ||
+ | <code bash> | ||
+ | gnuplot> plot " | ||
+ | </ | ||
+ | To plot the Potential energy: | ||
+ | <code bash> | ||
+ | gnuplot> plot " | ||
+ | </ | ||
+ | To plot the Temperature: | ||
+ | <code bash> | ||
+ | gnuplot> plot " | ||
+ | </ | ||
+ | |||
+ | |||
+ | </ | ||
+ | |||
+ | Now you will perform | ||
+ | |||
+ | <note tip> | ||
+ | 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> | ||
+ | </ | ||
+ | |||
+ | In cp2k input files you should again have a look at the following section: | ||
+ | <code - md_part.inp.300> | ||
+ | & | ||
+ | ???????? ??? ! Please specify the appropriete ensemble for you MD simulation | ||
+ | ????? ?????? | ||
+ | ???????? ??? ! Please specify the length of an integration step | ||
+ | ??????????? ??? ! Please specify the temperature of the simulation | ||
+ | &?????????? | ||
+ | &???? | ||
+ | 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). | ||
<code bash> | <code bash> | ||
you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.100 -o out.100 | you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.100 -o out.100 | ||
</ | </ | ||
- | * Then, perform | + | * Then, perform |
<code bash> | <code bash> | ||
you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.300 -o out.300 | you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.300 -o out.300 | ||
Line 79: | Line 144: | ||
</ | </ | ||
- | Open Tk Console (Extensions menu > Tk console). And to define the two dihedrals (**PHI** and **PSI**) from there, you can enter: | + | * Open Tk Console (Extensions menu > Tk console). And to define the two dihedrals (**PHI** and **PSI**) from there, you can enter: |
<code tcl> | <code tcl> | ||
- | source " | + | vmd> |
</ | </ | ||
- | You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory. | + | You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory |
- | Using " | + | * Now using " |
+ | - Go to Graphics > Labels | ||
+ | - In the drop-down list chose Dihedrals | ||
+ | - Chose both dihedrals in the list | ||
+ | - Go to the " | ||
+ | - Press on the " | ||
+ | - (Optional) save these graps in a text file (File > Export to ASCII matrix...) | ||
- | < | + | < |
+ | Which differences do you notice between the nve, the 100 K and the 300 K case? Can you explain them? | ||
+ | </ | ||
exercises/2015_ethz_mmm/md_ala.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1