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 revision | ||
exercises:2015_ethz_mmm:md_ala [2015/03/11 09:44] – yakutovich | exercises:2015_ethz_mmm:md_ala [2020/08/21 10:15] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
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 35: | Line 38: | ||
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> | ||
& | & | ||
- | ???????? ??? ! Please | + | ???????? ??? ! Please |
- | ????? ?????? | + | ????? ?????? |
- | ???????? ???? ??? ! Please | + | ???????? ???? ??? ! Please |
- | ??????????? ????? ! Please | + | ??????????? ????? ! Please |
&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 | + | <note tip> |
+ | Assignments: | ||
+ | - We are performing MD at a constant energy, but why we still have to define the temperature? | ||
+ | </ | ||
+ | |||
+ | * Make four copies of the previous | ||
+ | * 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 | ||
+ | </ | ||
* Have a look at the corresponding *.ener files (we suggest you to use gnuplot). | * Have a look at the corresponding *.ener files (we suggest you to use gnuplot). | ||
<note tip> | <note tip> | ||
Assignments | Assignments | ||
- Do you see the energy conservation? | - Do you see the energy conservation? | ||
- | - Describe | + | - Analyse |
</ | </ | ||
Line 83: | Line 105: | ||
</ | </ | ||
- | In cp2k input file it can be specified as follows: | + | In cp2k input files you should again have a look at the following section: |
<code - md_part.inp.300> | <code - md_part.inp.300> | ||
& | & | ||
- | | + | |
- | | + | |
- | | + | |
- | | + | |
- | &THERMOSTAT | + | &?????????? |
- | &NOSE ! This section | + | &???? ! Please put here a section |
TIMECON 50 ! Timeconstant of the thermostat chain | TIMECON 50 ! Timeconstant of the thermostat chain | ||
- | | + | LENGTH 3 ! Length of the Nose-Hoover chain |
- | &END | + | YOSHIDA 3 ! Order of the yoshida integretor used for the thermostat |
+ | | ||
+ | &??? | ||
&END MD | &END MD | ||
</ | </ | ||
- | The first simulation is done at 100 K: | + | 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 123: | Line 147: | ||
<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 (Extensions> | You can also pick from the extensions the "RMSD trajectory tool" and use it to align the molecule along the trajectory (Extensions> | ||
- | * Now 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 "Graph..." button | ||
+ | - (Optional) save these graps in a text file (File > Export to ASCII matrix...) | ||
<note tip> | <note tip> |
exercises/2015_ethz_mmm/md_ala.1426067067.txt.gz · Last modified: 2020/08/21 10:14 (external edit)