PLUMED-NEST

Project ID: plumID:19.028
Source: Lysozyme/round2/plumed.2.dat
Originally used with PLUMED version: 2.3
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

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
=1-2881


lig: 
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
=2870,2872,2874


d1: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=lig,1533
The DISTANCE action with label d1 calculates a scalar quantityd2: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=lig,1716
The DISTANCE action with label d2 calculates a scalar quantityd3: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=lig,2285
The DISTANCE action with label d3 calculates a scalar quantityd4: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=lig,2005
The DISTANCE action with label d4 calculates a scalar quantityd5: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=lig,1905
The DISTANCE action with label d5 calculates a scalar quantityd6: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=lig,2239 
The DISTANCE action with label d6 calculates a scalar quantityd7: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=lig,2424
The DISTANCE action with label d7 calculates a scalar quantityd8: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=lig,2523

The DISTANCE action with label d8 calculates a scalar quantityhelix1: 
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
=1416,1428,1452,1475,1501,1513,1533,1554,1566
helix2: 
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
=1964,1980,1994,2005,2028,2052,2071,2094,2111
helix3: 
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
=2176,2200,2212,2227,2239,2251,2271,2285,2308
helix4: 
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
=2535,2559,2583,2603,2626,2642,2658,2678,2702

hd12: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=helix1,helix2
The DISTANCE action with label hd12 calculates a scalar quantityhd23: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=helix2,helix3
The DISTANCE action with label hd23 calculates a scalar quantityhd34: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=helix3,helix4


The DISTANCE action with label hd34 calculates a scalar quantity
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=rc1 
ARG
the input to this function
=d1,d2,d3,d4,d5,d6,d7,d8,hd12,hd23,hd34  
POWERS
 the powers to which you are raising each of the arguments in your function
=1,1,1,1,1,1,1,1,1,1,1 
COEFFICIENTS
 the coefficients of the arguments in your function
=-0.24184742797183606,-0.18979446447575038,0.30815019411555283,-0.22502483535326306,0.047142102936704726,0.1788708396613595,-0.21220396475862427,-0.35463776722562945,-0.11036762633847245,0.13131908514789475,0.7248819389103112 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO




EXTERNAL
Calculate a restraint that is defined on a grid that is read during start up More details
 
ARG
the input for this action is the scalar output from one or more other actions
=rc1 
FILE
the name of the file containing the external potential
=static_bias.2.txt 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=external1


The EXTERNAL action with label external1 calculates the following quantities:
 Quantity   
 Description  
external1.bias
the instantaneous value of the bias potential
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,hd12,hd23,hd34,rc1,external1.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=benzene_Lyso_T298_2