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
# Define orientational vectors and anglesDISTANCE...Calculate the distance between a pair of atoms. More detailsATOMS1=6,10the pair of atom that we are calculating the distance betweenATOMS2=39,43the pair of atom that we are calculating the distance betweenATOMS3=72,76the pair of atom that we are calculating the distance betweenATOMS4=105,109 ...the pair of atom that we are calculating the distance betweenATOMS285=9378,9382the pair of atom that we are calculating the distance betweenATOMS286=9411,9415the pair of atom that we are calculating the distance betweenATOMS287=9444,9448the pair of atom that we are calculating the distance betweenATOMS288=9477,9481the pair of atom that we are calculating the distance betweenLABEL=dd_mo1a label for the action so that its output can be referenced in the input to other actionsCOMPONENTS... 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 ... DISTANCEThis action is not part of PLUMED and was included by using a LOAD command More details
vv_mo2:NORMALIZEARG1=dd_mo2.x ARG2=dd_mo2.y ARG3=dd_mo2.z dp_mat_mo2:This action is not part of PLUMED and was included by using a LOAD command More detailsDOTPRODUCT_MATRIXGROUP1=vv_mo2.x GROUP2=vv_mo2.y GROUP3=vv_mo2.z ang_mat_mo2:This action is not part of PLUMED and was included by using a LOAD command More detailsMATHEVALAn alias to the ef CUSTOM function. More detailsARG1=dp_mat_mo2the input to this functionFUNC=acos(xthe function you wish to evaluatePERIODIC=NOif the output of your function is periodic then you should specify the periodicity of the function
# Plot Distribution valg_mo:KDECreate a histogram from the input scalar/vector/matrix using KDE More detailsARG1=ang_mat_mo1the input for this action is the scalar output from one or more other actionsARG2=ang_mat_mo2the input for this action is the scalar output from one or more other actionsGRID_MIN=0.000,0.000the lower bounds for the gridGRID_MAX=3.142,3.142the upper bounds for the gridGRID_BIN=37,37the number of bins for the gridBANDWIDTH=0.250,0.250the bandwidths for kernel density esimtationKERNEL=GAUSSIANthe kernel function you are usingPrint quantities to a file. More detailsARG=valg_mothe input for this action is the scalar output from one or more other actionsFILE=plumed_md_mo.datthe name of the file on which to output these quantities