PLUMED-NEST-TEST-SITE

Project ID: plumID:24.028
Source: inputs/tip3p/U/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

# 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
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis 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=11,14,18
gh11The GHOST action with label gh11 calculates the following quantities:
 Quantity   
 Type   
 Description  
gh11
atoms
virtual atom calculated by GHOST action: 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=11,14,18 COORDINATEScoordinates of the ghost atom in the local reference frame=0,1,0
gh12The GHOST action with label gh12 calculates the following quantities:
 Quantity   
 Type   
 Description  
gh12
atoms
virtual atom calculated by GHOST action:  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=11,14,18 COORDINATEScoordinates of the ghost atom in the local reference frame=0,0,0
norm1The DISTANCE action with label norm1 calculates the following quantities:
 Quantity   
 Type   
 Description  
norm1.x
scalar
the x-component of the vector connecting the two atoms
norm1.y
scalar
the y-component of the vector connecting the two atoms
norm1.z
scalar
the z-component of the vector connecting the two atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=gh11,gh12 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 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