Project ID: plumID:24.028
Source: inputs/tip3p/A2/metadyn/plumed_orientation.dat
Originally used with PLUMED version: 2.9
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
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# Activate MOLINFO functionalities MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=../conf.pdb WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=11,15,20 ENTITY1the atoms that make up a molecule that you wish to align=44,48,53 gh11: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11,15,20 COORDINATEScoordinates of the ghost atom in the local reference frame=0,1,0 gh12: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=11,15,20 COORDINATEScoordinates of the ghost atom in the local reference frame=0,0,0 norm1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=gh12,gh11 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
gh21: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=44,48,53 COORDINATEScoordinates of the ghost atom in the local reference frame=0,1,0 gh22: GHOSTCalculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=44,48,53 COORDINATEScoordinates of the ghost atom in the local reference frame=0,0,0 norm2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=gh22,gh21 COMPONENTS calculate the x, y and z components of the distance separately and store them as label
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=norm1.z,norm2.z FILEthe name of the file on which to output these quantities=ANALYSIS_NORMAL STRIDE the frequency with which the quantities of interest should be output=1