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
tested onv2.8
tested onmaster
# Define orientational vectors and angles
DISTANCE
Calculate the distance between a pair of atoms. More details
...
ATOMS1
the pair of atom that we are calculating the distance between
=6,10
ATOMS2
the pair of atom that we are calculating the distance between
=39,43
ATOMS3
the pair of atom that we are calculating the distance between
=72,76
ATOMS4
the pair of atom that we are calculating the distance between
=105,109 ...
ATOMS285
the pair of atom that we are calculating the distance between
=9378,9382
ATOMS286
the pair of atom that we are calculating the distance between
=9411,9415
ATOMS287
the pair of atom that we are calculating the distance between
=9444,9448
ATOMS288
the pair of atom that we are calculating the distance between
=9477,9481
LABEL
a label for the action so that its output can be referenced in the input to other actions
=dd_mo1
COMPONENTS
This 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:
NORMALIZE
This 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_MATRIX
This 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:
MATHEVAL
An alias to the ef CUSTOM function. More details
ARG1
the input for this action is the scalar output from one or more other actions
=dp_mat_mo2
FUNC
the function you wish to evaluate
=acos(x
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
# Plot Distribution valg_mo:
KDE
This action is not part of PLUMED and was included by using a LOAD command More details
ARG1=ang_mat_mo1 ARG2=ang_mat_mo2 GRID_MIN=0.000,0.000 GRID_MAX=3.142,3.142 GRID_BIN=37,37 BANDWIDTH=0.250,0.250 KERNEL=GAUSSIAN
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=valg_mo
FILE
the name of the file on which to output these quantities
=plumed_md_mo.dat