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exercises:2015_ethz_mmm:c2h2_bond_energy

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# C2H2 and C2H4 bond energy

Before you start it is ABSOLUTELY NEСESSARY to update the function library. So from you $HOME directory please run: you@eulerX ~$ ./update_functionlibrary

Pay attention to the output of this program. It may give you some helpful information

If you don't have the file “update_functionlibrary” please download it from here update_functionlibrary.zip and unzip into your $HOME directory you@eulerX ~$ unzip update_functionlibrary.zip
you@eulerX ~$chmod 755 update_functionlibrary Or if you are working on the remote computer you can also do the following: you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:update_functionlibrary.zip
you@eulerX ~$unzip exercises:2015_ethz_mmm:update_functionlibrary.zip you@eulerX ~$ chmod 755 update_functionlibrary
REMEMBER to load the module for the cp2k program:
you@eulerX ~$module load new cp2k and to submit the job chain: you@eulerX ~$ bsub < c2h2.a.chain

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 ~$unzip exercises:2015_ethz_mmm:exercise_2.1.zip All files of this exercise (input and scripts are all commented) can be downloaded from the wiki: exercise_2.1.zip In this exercise you will test the general AMBER force field, which is suitable for a large class of molecules. In this example you will compute the classical energy of a simple acetylene molecule and apply small variations to the C-C bond lengths. Then go to the directory “exercise_2.1/c2h2/”. you@eulerX ~$ cd exercise_2.1/c2h2/

The input file structure of the template is the following:

c2h2.inp.templ
&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:

c2h2.chain
#
# 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: change replace getcolumn add list
#
module load new cp2k
. ~/Scripts/myfunctions.bash

#
# deletes old output file
#
rm curve.amber.c2h2

#
# loop over all values of n
#

for n in list -5 5
do
dist_cc=change $dist_cc0$n $delta c2=add$dist_hc $dist_cc  h2=add$c2 $dist_hc  # # replaces coordinates in the input # replace _C1_$dist_hc < c2h2.amber.inp.templ | replace _C2_ $c2 | replace _H2_$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= getcolumn 'ENERGY|' 9 < c2h2.$dist_cc.out  echo$dist_cc $energy >> curve.amber.c2h2 # # loop over n # done # # Cleaning... # mkdir Logs mv c2h2.*.inp c2h2.*.out Logs rm RUN* *restart* At this point submit the job grid, first loading the module for cp2k entering you@brutusX mmm_exercise_2.1$ module load new cp2k
you@brutusX mmm_exercise_2.1$bsub < c2h2.chain Finally, the gnuplot code to fit the curve to a parabolic function - and to extract the parameters of the bond interaction is the following you@brutusX mmm_exercise_2.1$ gnuplot fit.gnu
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 ~$cd ../c2h4 • The new input c2h4.inp.templ is similar to the previous one, only with different project name (C2H4) and coordinates: H 0 3.06 0 H 0 4.94 0 C _C1_ 4.0 0 C _C2_ 4.0 0 H _H3_ 3.06 0 H _H3_ 4.94 0  • The script to modify the bond lengths changes slightly as well c2h4.chain # # task 2.2 C2H4 bond strength # # the initial deltax of C, C, H, H # and increment delta # dist_hcx=0.560 dist_cc0=1.324 delta=0.002 # # loads the functions # this script uses the functions: change replace getcolumn add list # module load new cp2k . ~/Scripts/myfunctions.bash # # deletes old output file # rm curve.amber.c2h4 # # loop over all values of n # for n in list -5 5 do dist_cc=change$dist_cc0 $n$delta
c2=add $dist_hcx$dist_cc
h3=add $c2$dist_hcx 
#
# replaces coordinates in the input
#
replace _C1_ $dist_hcx < c2h4.amber.inp.templ | replace _C2_$c2  | 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.$dist_cc.out # # gets the energy from the output (in a.u.) # energy= getcolumn 'ENERGY|' 9 < c2h4.$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*

• Use a fitting gnuplot script to verify the value of the parameters. What has changed with respect to the C2H2 case? Why?
Assignment:
1. Report the values of the bond length and force constants in all cases.
2. Discuss these values in view of the kind of molecules we are simulatin
exercises/2015_ethz_mmm/c2h2_bond_energy.1424964787.txt.gz · Last modified: 2015/02/26 15:33 by yakutovich