PLUMED-NEST

Project ID: plumID:19.075
Source: regtest/pycv/rt-f2/plumed.dat
Originally used with PLUMED version: 2.5.2-mod
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

# Copy of basic/rt13

g1: 
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
=1-10
c1: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
   
ATOMS
the list of atoms which are involved the virtual atom's definition
=g1

t1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=1,6,10,15
The TORSION action with label t1 calculates a scalar quantityt2: 
TORSION
Calculate a torsional angle. More details
 
VECTOR1
two atoms that define a vector
=6,1 
AXIS
two atoms that define an axis
=6,10 
VECTOR2
two atoms that define a vector
=10,15
The TORSION action with label t2 calculates a scalar quantityt3: 
TORSION
Calculate a torsional angle. More details
 
VECTOR1
two atoms that define a vector
=6,1 
AXIS
two atoms that define an axis
=20,7 
VECTOR2
two atoms that define a vector
=10,c1

The TORSION action with label t3 calculates a scalar quantitycc1: 
PYTHONFUNCTION
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=t1,t2,t3 IMPORT=pythonfunction FUNCTION=cc1 PERIODIC=NO
cc2: 
PYTHONFUNCTION
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=t1,t2,t3 IMPORT=pythonfunction FUNCTION=cc2 PERIODIC=NO
cc3: 
PYTHONFUNCTION
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG=t1,t2    IMPORT=pythonfunction FUNCTION=cc3 PERIODIC=NO

# cc1: MATHEVAL ARG=t1,t2,t3 FUNC=x^2+y+0*z+1 PERIODIC=NO
# cc2: MATHEVAL ARG=t1,t2,t3 FUNC=0*x^3+0*y^3+0*z^3 PERIODIC=NO
# cc3: MATHEVAL ARG=t1,t2 FUNC=x^2+y^2 PERIODIC=NO

all: 
CUSTOM
Calculate a combination of variables using a custom expression. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=t1,t2,t3,cc1,cc2,cc3 
VAR
the names to give each of the arguments in the function
=a1,a2,a3,a4,a5,a6 
FUNC
the function you wish to evaluate
={ (a1+a2+a3+a4+a5+a6) / 6.0 } 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The CUSTOM action with label all calculates a scalar quantity
RESTRAINT
Adds harmonic and/or linear restraints on one or more variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=all 
AT
the position of the restraint
=0 
SLOPE
 specifies that the restraint is linear and what the values of the force constants on each of the variables are
=1.0

The RESTRAINT action with label  calculates the following quantities:
 Quantity   
 Description  
.bias
the instantaneous value of the bias potential
.force2
the instantaneous value of the squared force due to this bias potential
PRINT
Print quantities to a file. More details
 ...
  
STRIDE
 the frequency with which the quantities of interest should be output
=2
  
ARG
the input for this action is the scalar output from one or more other actions
=t1,t2,t3,cc1,cc2,cc3,all
  
FILE
the name of the file on which to output these quantities
=COLVAR 
FMT
the format that should be used to output real numbers
=%6.5f
... PRINT

ENDPLUMED
Terminate plumed input. More details