exercises:2015_ethz_mmm:md_ala
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exercises:2015_ethz_mmm:md_ala [2015/03/09 15:15] – yakutovich | exercises:2015_ethz_mmm:md_ala [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
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<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 | ||
</ | </ | ||
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- | <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> | ||
- | </ | ||
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<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:// | ||
+ | </ | ||
+ | |||
+ | * 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 | ||
</ | </ | ||
+ | <note tip> | ||
+ | Assignments: | ||
+ | - We are performing MD at a constant energy, but why we still have to define the temperature? | ||
+ | </ | ||
- | * Perform a constant energy simulation, 100000 time steps, with a time step of 1 fs. | + | * Make four copies of the previous input file (say inp.nve_0.1, inp.nve_2.0, inp.nve_3.0, |
+ | * Perform the simulations with all these input files: | ||
<code bash> | <code bash> | ||
- | you@eulerX | + | you@eulerX |
+ | 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 | ||
</ | </ | ||
- | | + | |
- | - Access | + | <note tip> |
- | <note important> | + | Assignments |
+ | - Do you see the energy conservation? | ||
+ | - Analyse | ||
+ | </ | ||
- | - Perform now a constant Temperature simulation. The system is in contact with a thermostat, and the conserved quantity includes the thermostat degrees of freedom. The first simulation is done at 100 K: **inp.100** | + | <note important> |
- | - Then, perform a simulation at 300 K, using the restart file from the previous simulation: **inp.300**. | + | Hint (plotting |
- | - Now you have some outputs to study with vmd. | + | |
- | The trajectory files we are going to study are | + | 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 a constant Temperature simulations, | ||
+ | |||
+ | <note tip> | ||
+ | Concerning temperature control, in these exercises | ||
+ | </ | ||
+ | |||
+ | 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). The first simulation is done at 100 K: | ||
+ | <code bash> | ||
+ | you@eulerX exercise_4.1$ bsub cp2k.popt -i inp.100 -o out.100 | ||
+ | </ | ||
+ | * 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, but **put 300 K** instead of 100 K | ||
+ | <code bash> | ||
+ | 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.100-pos-1.pdb | ||
md.300-pos-1.pdb | md.300-pos-1.pdb | ||
</ | </ | ||
- | " | + | * Open (for example) nve_md-pos-1.pdb |
- | From the Extensions menu, you can choose the Tk console. And from there, you can enter | + | |
- | < | + | < |
+ | vmd nve_md-pos-1.pdb | ||
+ | </ | ||
- | which will define the two dihedrals | + | * Open Tk Console (Extensions menu > Tk console). And to define the two dihedrals |
- | You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory. Remember to replace " | + | |
- | Using "Labels" | + | <code tcl> |
+ | vmd> source | ||
+ | </ | ||
- | < | + | You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory (Extensions> |
+ | |||
+ | * 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