PLUMED-NEST

Project ID: plumID:19.058
Source: plumed_cylinder.dat
Originally used with PLUMED version: 2.5
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

# com1 is the COM of one triangular face of the prism, com2 of the other. The orientation is given by the vector from com1 to com2 
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
=3,25,39 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=com1
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
=49,69,81 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=com2

# inplane distance between com1 and com2
d1: 
INPLANEDISTANCES
Calculate the distance between a pair of atoms in the plane More details
 
VECTORSTART
The first atom position that is used to define the normal to the plane of interest
=com1 
VECTOREND
The second atom position that is used to defin the normal to the plane of interest
=com2 
GROUP
calculate distance for each distinct set of three atoms in the group
=1-162 
MIN
calculate the minimum value
={BETA=5} 

MOVINGRESTRAINT
Add a time-dependent, harmonic restraint on one or more variables. More details
 ...
    
ARG
the input for this action is the scalar output from one or more other actions
=d1.min
    
STEP0
This keyword appears multiple times as STEP$x$ with x=0,1,2,
=0      
AT0
AT$x$ is equal to the position of the restraint at time STEP$x$
=0.5  
KAPPA0
KAPPA$x$ is equal to the value of the force constants at time STEP$x$
=0.0
    
STEP1
This keyword appears multiple times as STEP$x$ with x=0,1,2,
=20000  
AT1
AT$x$ is equal to the position of the restraint at time STEP$x$
=0.5  
KAPPA1
KAPPA$x$ is equal to the value of the force constants at time STEP$x$
=50000.0
    
LABEL
a label for the action so that its output can be referenced in the input to other actions
=m1
    
VERSE
 Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than the restraint or whether it is acting on both sides (B)
=L
... MOVINGRESTRAINT

The MOVINGRESTRAINT action with label m1 calculates the following quantities:
 Quantity   
 Description  
m1.bias
the instantaneous value of the bias potential
m1.work
the total work performed changing this restraint
m1.force2
the instantaneous value of the squared force due to this bias potential
m1._cntr
one or multiple instances of this quantity can be referenced elsewhere in the input file
m1._work
one or multiple instances of this quantity can be referenced elsewhere in the input file
m1._kappa
one or multiple instances of this quantity can be referenced elsewhere in the input file
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.*,m1 
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
=10
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
=10