PLUMED-NEST

Project ID: plumID:23.040
Source: plumed_metad/plumed_reso.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
=0.001  #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 somethingcom1: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=cal1
The COM action with label com1 calculates somethingcom2: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=cal2
The COM action with label com2 calculates somethingcom3: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=cal3
The COM action with label com3 calculates somethingcom4: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=cal4
The COM action with label com4 calculates somethingcom5: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=cal5
The COM action with label com5 calculates somethingcom6: 
COM
Calculate the center of mass for a group of atoms. More details
 
ATOMS
the list of atoms which are involved the virtual atom's definition
=cal6

The COM action with label com6 calculates somethingd1:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com1,com2
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com1,com3
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com1,com4
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com1,com5
The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsd5:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com1,com6
The DISTANCE action with label d5 calculates the following quantities:
 Quantity   
 Description  
d5.value
the DISTANCE between this pair of atomsd6:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com2,com3
The DISTANCE action with label d6 calculates the following quantities:
 Quantity   
 Description  
d6.value
the DISTANCE between this pair of atomsd7:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com2,com4
The DISTANCE action with label d7 calculates the following quantities:
 Quantity   
 Description  
d7.value
the DISTANCE between this pair of atomsd8:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com2,com5
The DISTANCE action with label d8 calculates the following quantities:
 Quantity   
 Description  
d8.value
the DISTANCE between this pair of atomsd9:  
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com2,com6
The DISTANCE action with label d9 calculates the following quantities:
 Quantity   
 Description  
d9.value
the DISTANCE between this pair of atomsd10: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com3,com4
The DISTANCE action with label d10 calculates the following quantities:
 Quantity   
 Description  
d10.value
the DISTANCE between this pair of atomsd11: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com3,com5
The DISTANCE action with label d11 calculates the following quantities:
 Quantity   
 Description  
d11.value
the DISTANCE between this pair of atomsd12: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com3,com6
The DISTANCE action with label d12 calculates the following quantities:
 Quantity   
 Description  
d12.value
the DISTANCE between this pair of atomsd13: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com4,com5
The DISTANCE action with label d13 calculates the following quantities:
 Quantity   
 Description  
d13.value
the DISTANCE between this pair of atomsd14: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com4,com6
The DISTANCE action with label d14 calculates the following quantities:
 Quantity   
 Description  
d14.value
the DISTANCE between this pair of atomsd15: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=com5,com6

The DISTANCE action with label d15 calculates the following quantities:
 Quantity   
 Description  
d15.value
the DISTANCE between this pair of atoms
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
=mul_dist
  
ATOMS1
the pairs of atoms that you would like to calculate the angles for
=com1,com2 
  
ATOMS2
the pairs of atoms that you would like to calculate the angles for
=com1,com3
  
ATOMS3
the pairs of atoms that you would like to calculate the angles for
=com1,com4 
  
ATOMS4
the pairs of atoms that you would like to calculate the angles for
=com1,com5
  
ATOMS5
the pairs of atoms that you would like to calculate the angles for
=com1,com6
  
ATOMS6
the pairs of atoms that you would like to calculate the angles for
=com2,com3
  
ATOMS7
the pairs of atoms that you would like to calculate the angles for
=com2,com4
  
ATOMS8
the pairs of atoms that you would like to calculate the angles for
=com2,com5
  
ATOMS9
the pairs of atoms that you would like to calculate the angles for
=com2,com6
  
ATOMS10
the pairs of atoms that you would like to calculate the angles for
=com3,com4
  
ATOMS11
the pairs of atoms that you would like to calculate the angles for
=com3,com5
  
ATOMS12
the pairs of atoms that you would like to calculate the angles for
=com3,com6
  
ATOMS13
the pairs of atoms that you would like to calculate the angles for
=com4,com5
  
ATOMS14
the pairs of atoms that you would like to calculate the angles for
=com4,com6
  
ATOMS15
the pairs of atoms that you would like to calculate the angles for
=com5,com6
  
BETWEEN1
calculate the number of values that are within a certain range
={GAUSSIAN LOWER=9.   UPPER=12.5}
  
BETWEEN2
calculate the number of values that are within a certain range
={GAUSSIAN LOWER=13.  UPPER=17}
... DISTANCES

# Metadynamics
The DISTANCES action with label mul_dist calculates something
METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
ARG
the input for this action is the scalar output from one or more other actions
=mul_dist.between-1,mul_dist.between-2
GRID_MIN
the lower bounds for the grid
=0,0
GRID_MAX
the upper bounds for the grid
=20,20
SIGMA
the widths of the Gaussian hills
=0.1,0.1
HEIGHT
the heights of the Gaussian hills
=1.5
BIASFACTOR
use well tempered metadynamics and use this bias factor
=30
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
CALC_RCT
 calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
PACE
the frequency for hill addition
=500 # 1ps
... METAD


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
metad.rbias
the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct]
metad.rct
the reweighting factor c(t)
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=mul_dist.between-1,mul_dist.between-2,metad 
FILE
the name of the file on which to output these quantities
=metad_data.dat 
STRIDE
 the frequency with which the quantities of interest should be output
=500
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15 
FILE
the name of the file on which to output these quantities
=COLVAR 
STRIDE
 the frequency with which the quantities of interest should be output
=500

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
=500