PLUMED-NEST-TEST-SITE

Project ID: plumID:21.019
Source: Ibuprofen_Overprediction/plumed_mo.dat
Originally used with PLUMED version: 2.5-mod
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

# Define orientational vectors and angles
DISTANCECalculate the distance/s between pairs of atoms. More details ...
ATOMS1the pair of atom that we are calculating the distance between=6,10
ATOMS2the pair of atom that we are calculating the distance between=39,43
ATOMS3the pair of atom that we are calculating the distance between=72,76
ATOMS4the pair of atom that we are calculating the distance between=105,109
...
ATOMS285the pair of atom that we are calculating the distance between=9378,9382
ATOMS286the pair of atom that we are calculating the distance between=9411,9415
ATOMS287the pair of atom that we are calculating the distance between=9444,9448
ATOMS288the pair of atom that we are calculating the distance between=9477,9481
LABELa label for the action so that its output can be referenced in the input to other actions=dd_mo1
The DISTANCE action with label dd_mo1 calculates the following quantities:
 Quantity   
 Description  
dd_mo1.value
the DISTANCE between this pair of atomsCOMPONENTSThis action is not part of PLUMED and was included by using a LOAD command More details
... DISTANCE

vv_mo1 NORMALIZE ARG1=dd_mo1.x ARG2=dd_mo1.y ARG3=dd_mo1.z
dp_mat_mo1 DOTPRODUCT_MATRIX GROUP1=vv_mo1.x GROUP2=vv_mo1.y GROUP3=vv_mo1.z
ang_mat_mo1 MATHEVAL ARG1=dp_mat_mo1 FUNC=acos(x) PERIODIC=NO

DISTANCE ...
ATOMS1=18,20
ATOMS2=51,53
ATOMS3=84,86
ATOMS4=117,119
...
ATOMS285=9390,9392
ATOMS286=9423,9425
ATOMS287=9456,9458
ATOMS288=9489,9491
LABEL=dd_mo2
COMPONENTS
... DISTANCE

vv_mo2: NORMALIZEThis action is not part of PLUMED and was included by using a LOAD command More details ARG1=dd_mo2.x ARG2=dd_mo2.y ARG3=dd_mo2.z
dp_mat_mo2: DOTPRODUCT_MATRIXThis action is not part of PLUMED and was included by using a LOAD command More details GROUP1=vv_mo2.x GROUP2=vv_mo2.y GROUP3=vv_mo2.z
ang_mat_mo2: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARG1=dp_mat_mo2 FUNCthe function you wish to evaluate=acos(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Plot Distribution
The MATHEVAL action with label ang_mat_mo2 calculates the following quantities:
 Quantity   
 Description  
ang_mat_mo2.value
an arbitrary functionvalg_mo: KDECreate a histogram from the input scalar/vector/matrix using KDE More details ARG1=ang_mat_mo1 ARG2=ang_mat_mo2  GRID_MIN the lower bounds for the grid=0.000,0.000 GRID_MAX the upper bounds for the grid=3.142,3.142 GRID_BINthe number of bins for the grid=37,37 BANDWIDTHthe bandwidths for kernel density esimtation=0.250,0.250 KERNEL the kernel function you are using=GAUSSIAN
The KDE action with label valg_mo calculates the following quantities:
 Quantity   
 Description  
valg_mo.value
a function on a grid that was obtained by doing a Kernel Density Estimation using the input argumentsPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=valg_mo FILEthe name of the file on which to output these quantities=plumed_md_mo.dat