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 2.1 exercise into your $HOME folder and unzip it.
you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_2.1.zip you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_2.1.zip
In this exercise you will test the general AMBER force field, which is suitable for a large class of molecules. In this example you will compute the classical energy of a simple acetylene molecule and apply small variations to the C-C bond lengths.
Then go to the directory “exercise_2.1/c2h2/”.
you@eulerX ~$ cd exercise_2.1/c2h2/
The input file structure of the template is the following:
&FORCE_EVAL ! This section defines method for calculating energy and forces
METHOD FIST ! Using Molecular Mechanics
&MM
&FORCEFIELD ! This section specifies forcefield parameters
parm_file_name c2h2.top
! This file contains force field parameters
parmtype AMBER
&SPLINE ! This section specifies parameters to set up the splines used in the nonboned interactions (both pair body potential and many body potential)
EMAX_SPLINE 15.0 ! Specify the maximum value of the potential up to which splines will be constructed
&END
&END FORCEFIELD
&POISSON ! This section specifies parameters for the Poisson solver
&EWALD ! This section specifies parameters for the EWALD summation method (for the electrostatics)
EWALD_TYPE SPME ! Smooth particle mesh using beta-Euler splines
ALPHA .36
GMAX 128 ! Number of grid points
&END EWALD
&END POISSON
&PRINT ! This section controls printing options
&FF_INFO
&END
&FF_PARAMETER_FILE
&END
&END
&END MM
&SUBSYS ! This section defines the system
&CELL ! Unit cell set up
ABC 50 50 50 ! Lengths of the cell vectors A, B, and C
&END CELL
&COORD ! This section specify all the atoms and their coordinates
H 0 0 0
C _C1_ 0 0
C _C2_ 0 0
H _H2_ 0 0
&END COORD
&TOPOLOGY
CHARGE_BETA ! Read MM charges from the BETA field of PDB file
CONNECTIVITY AMBER ! Use AMBER topology file for reading connectivity
CONN_FILE_NAME c2h2.top
! This file contains connectivity data
&END TOPOLOGY
&PRINT
&TOPOLOGY_INFO
AMBER_INFO
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL ! Section with general information regarding which kind of simulation to perform an parameters for the whole PROGRAM
PRINT_LEVEL LOW ! Global print level
PROJECT c2h2 ! Name of the project. This word will appear as part of a name of all ouput files (except main ouput file, specified with -o option)
RUN_TYPE ENERGY ! Calculating of energy for the fixed position of atoms
&END GLOBAL
The script to modify the C-C distance in the input and generate the curve is the following:
# # task 2.1 C2H2 bond strength # # the distances of equilibrium # and increment delta # dist_cc0=1.181 dist_hc=1.066 delta=0.0002 # # loads the functions # this script uses the functions: m_change m_replace m_getcolumn m_sum m_list # module load new cp2k . /cluster/apps/courses/mmm/m_functions.bash # # deletes old output file # rm curve.amber.c2h2 # # loop over all values of n # for n in `m_list -5 5` do dist_cc=`m_change $dist_cc0 $n $delta` c2=`m_sum $dist_hc $dist_cc` h2=`m_sum $c2 $dist_hc ` # # replaces coordinates in the input # m_replace _C1_ $dist_hc < c2h2.inp.templ | m_replace _C2_ $c2 | m_replace _H2_ $h2 > c2h2.$dist_cc.inp # # Runs cp2k # echo RUNNING cp2k with the input c2h2.$dist_cc.inp # bsub -n 1 mpirun cp2k.popt -i c2h2.$dist_cc.inp > c2h2.$dist_cc.out cp2k.popt -i c2h2.$dist_cc.inp > c2h2.$dist_cc.out # # gets the energy from the output (in a.u.) # energy=` m_getcolumn 'ENERGY|' 9 < c2h2.$dist_cc.out ` echo $dist_cc $energy >> curve.amber.c2h2 # # loop over n # done # # Cleaning... # mkdir Logs mv c2h2.*.inp c2h2.*.out Logs rm RUN* *restart*
At this point submit the job grid, first loading the module for cp2k entering
you@eulerX c2h2$ module load new cp2k you@eulerX c2h2$ bsub < c2h2.chain
Finally, the gnuplot code to fit the curve to a parabolic function - and to extract the parameters of the bond interaction is the following
you@eulerX c2h2$ gnuplot fit.gnu
#!/usr/bin/gnuplot f(x)=k*(x-x0)*(x-x0)+e0 # definition of the function to be fitted delta = 0.002 # e0=0.007720330647107 # initial value of e0 k = 500 # initial value of k x0=1 # initial value of x0 #a0 = 1.3327436840 # set xlabel 'd (Angstrom)' # label of the x-axis set ylabel 'E (kcal/mol)' # label of the y-axis set title "c2h2 triple bond" # main title fit f(x) 'curve.a.c2h2' u ($1):(($2)*627) via k,x0,e0 # fitting procedure # ^ function to be fitted # ^ take data from the file curve.a.c2h2 # and use the first column as X and the second one # ax Y (all values of the second column are multiplied by 627. 1 Hartree = 627 kcal/mol) # ^ k, x0, e0 - are parameters to be adjusted plot 'curve.amber.c2h2' u ($1):(($2)*627)-e0 t 'computed AMBER' w lp lw 2 ps 2 pt 7, f(x)-e0 t 'k*(x-x0)^2' w l lw 2 # ^ take data for the first plot from the file curve.a.c2h2 # ^ use the firts column as X and the second as Y # ^ title of the first plot: computed AMBER # ^ draw points and lines # ^ line width = 2 # ^ point size = 2 # ^ point type = 7 # ^ plot function f(x)-e0 # ^ title of the second plot: k*(x-x0)^2 # ^ draw only line # ^ line width = 2 pause mouse # exit by right-clicking on the plot window # EOF
Compare the values that you obtain with the ones listed in the “human readable” potential file c2h2-force_field.pot that was generated by cp2k.
Now, perform the same exercise in another directory for the molecule C2H4.
you@eulerX c2h2$ cd ../c2h4
H 0 3.06 0 H 0 4.94 0 C _C1_ 4.0 0 C _C2_ 4.0 0 H _H3_ 3.06 0 H _H3_ 4.94 0
# # task 2.2 C2H4 bond strength # # the initial deltax of C, C, H, H # and increment delta # dist_hcx=0.560 dist_cc0=1.324 delta=0.002 # # loads the functions # this script uses the functions: m_change m_replace m_getcolumn m_sum m_list # module load new cp2k #. ~/Scripts/myfunctions.bash . /cluster/apps/courses/mmm/m_functions.bash # # deletes old output file # rm curve.amber.c2h4 # # loop over all values of n # for n in `m_list -5 5` do dist_cc=`m_change $dist_cc0 $n $delta` c2=`m_sum $dist_hcx $dist_cc` h3=`m_sum $c2 $dist_hcx ` # # replaces coordinates in the input # m_replace _C1_ $dist_hcx < c2h4.inp.templ | m_replace _C2_ $c2 | m_replace _H3_ $h3 > c2h4.$dist_cc.inp # # Runs cp2k # echo RUNNING cp2k with the input c2h4.$dist_cc.inp cp2k.popt -i c2h4.$dist_cc.inp > c2h4.$dist_cc.out # # gets the energy from the output (in a.u.) # energy=` m_getcolumn 'ENERGY|' 9 < c2h4.$dist_cc.out ` echo $dist_cc $energy >> curve.amber.c2h4 # # loop over n # done # # Cleaning... # mkdir Logs mv c2h4.*.inp c2h4.*.out Logs rm RUN* *restart*