PLUMED-NEST

Project ID: plumID:23.040
Source: plumed_analysis/resorcinarene/plumed_solvent.dat
Originally used with PLUMED version: 2.6
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

UNITS
This command sets the internal units for the code. More details
 
LENGTH
the units of lengths
=A 
TIME
the units of time
=1  #Amstroeng, hartree, fs

The UNITS action with label  calculates something
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-72 
ENTITY1
the atoms that make up a molecule that you wish to align
=73-144 
ENTITY2
the atoms that make up a molecule that you wish to align
=145-216 
ENTITY3
the atoms that make up a molecule that you wish to align
=217-288 
ENTITY4
the atoms that make up a molecule that you wish to align
=289-360 
ENTITY5
the atoms that make up a molecule that you wish to align
=361-432 
ENTITY6
the atoms that make up a molecule that you wish to align
=433-435 
ENTITY7
the atoms that make up a molecule that you wish to align
=436-438 
ENTITY8
the atoms that make up a molecule that you wish to align
=439-441 
ENTITY9
the atoms that make up a molecule that you wish to align
=442-444 
ENTITY10
the atoms that make up a molecule that you wish to align
=445-447 
ENTITY11
the atoms that make up a molecule that you wish to align
=448-450 
ENTITY12
the atoms that make up a molecule that you wish to align
=451-453 
ENTITY13
the atoms that make up a molecule that you wish to align
=454-456

# Group definition
cal1: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-72
The GROUP action with label cal1 calculates somethingcal2: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=73-144
The GROUP action with label cal2 calculates somethingcal3: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=145-216
The GROUP action with label cal3 calculates somethingcal4: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=217-288
The GROUP action with label cal4 calculates somethingcal5: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=289-360
The GROUP action with label cal5 calculates somethingcal6: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=361-432

The GROUP action with label cal6 calculates somethingcl3_com: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
NDX_FILE
the name of index file (gromacs syntax)
=index_files/com_cl3.ndx 
NDX_GROUP
the name of the group to be imported (gromacs syntax) - first group found is used by default
=CL3_COM

The GROUP action with label cl3_com calculates somethingcom1: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=cal1
The CENTER action with label com1 calculates somethingcom2: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=cal2
The CENTER action with label com2 calculates somethingcom3: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=cal3
The CENTER action with label com3 calculates somethingcom4: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=cal4
The CENTER action with label com4 calculates somethingcom5: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=cal5
The CENTER action with label com5 calculates somethingcom6: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=cal6

The CENTER action with label com6 calculates somethingcom_all: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=cal1,cal2,cal3,cal4,cal5,cal6

The CENTER action with label com_all calculates something
DISTANCES
Calculate the distances between multiple piars of atoms More details
 ...
  
LABEL
a label for the action so that its output can be referenced in the input to other actions
=inside_mol
  
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=com_all 
  
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=cl3_com
  
LESS_THAN
calculate the number of variables that are less than a certain target value
={RATIONAL R_0=6.5} 
... DISTANCES


The DISTANCES action with label inside_mol calculates something
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=inside_mol 
FILE
the name of the file on which to output these quantities
=solvent.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=1
FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1