PLUMED-NEST

Project ID: plumID:23.033
Source: plumed_inputs/parallel_hairpin_HBfix_plumed.dat
Originally used with PLUMED version: 2.5.6
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

# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details. 

MOLINFO
This command is used to provide information on the molecules that are present in your system. More details
 
STRUCTURE
a file in pdb format containing a reference structure
=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb
The MOLINFO 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
=1-293	

# HBfix SECTION
group_1: 
COORDINATION
Calculate coordination numbers. More details
 
PAIR
 Pair only 1st element of the 1st group with 1st element in the second, etc
 
GROUPA
First list of atoms
=21,18,54,51,87,84 
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=209,212,242,245,275,278 
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={CUSTOM FUNC=((-2092.0000000000)*(0.3-x)^2)*step(x-0.3)*step(0.4-x)+((-2092.0000000000)*(0.1)*(2*x-0.7))*step(x-0.4)+((2615.0000000000)*(0.3-x)^2)*step(x-0.3)*step(0.38-x)+((2615.0000000000)*(0.08)*(2*x-0.68))*step(x-0.38) R_0=1.0}

The COORDINATION action with label group_1 calculates the following quantities:
 Quantity   
 Description  
group_1.value
the value of the coordinationtot_1: 
COMBINE
Calculate a polynomial combination of a set of other variables. More details
 
ARG
the input to this function
=group_1 
COEFFICIENTS
 the coefficients of the arguments in your function
=
@replicas:
This keyword specifies that different replicas have different values for this quantity.  See here for more details.
{2.0000000,1.9092000,1.8225220,1.7397800,1.6607940,1.5853940,1.5134160,1.4447080,1.3791180,1.3165060,1.2567360,1.1996800} 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

The COMBINE action with label tot_1 calculates something
BIASVALUE
Takes the value of one variable and use it as a bias More details
 
ARG
the input for this action is the scalar output from one or more other actions
=tot_1 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=all_group_1

# biasing eRMSD:
The BIASVALUE action with label all_group_1 calculates the following quantities:
 Quantity   
 Description  
all_group_1.bias
the instantaneous value of the bias potential
all_group_1._bias
one or multiple instances of this quantity can be referenced elsewhere in the input fileDISTfull: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-9
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=3.2
The ERMSD action with label DISTfull calculates the following quantities:
 Quantity   
 Description  
DISTfull.value
the eRMSD between the instantaneous structure and the reference structure that was inputDISTg5end: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=3.2
The ERMSD action with label DISTg5end calculates the following quantities:
 Quantity   
 Description  
DISTg5end.value
the eRMSD between the instantaneous structure and the reference structure that was inputDISTg3end: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
ATOMS
the list of atoms (use lcs)
=
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-9
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb 
CUTOFF
 only pairs of atoms closer than CUTOFF are considered in the calculation
=3.2

The ERMSD action with label DISTg3end calculates the following quantities:
 Quantity   
 Description  
DISTg3end.value
the eRMSD between the instantaneous structure and the reference structure that was input
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
=DD  
ARG
the input to this function
=DISTfull,DISTg5end,DISTg3end 
COEFFICIENTS
 the coefficients of the arguments in your function
=6,-3,-3 
POWERS
 the powers to which you are raising each of the arguments in your function
=2,2,2 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The COMBINE action with label DD calculates something
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
=interD  
ARG
the input to this function
=DD 
POWERS
 the powers to which you are raising each of the arguments in your function
=0.5 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
COEFFICIENTS
 the coefficients of the arguments in your function
=0.40824829 #COEF=sqrt(1/6)

# eRMSD with standard cutoff (2.4), used for monitoring only:
The COMBINE action with label interD calculates somethingDIST1: 
ERMSD
Calculate eRMSD with respect to a reference structure. More details
 
ATOMS
the list of atoms (use lcs)
=
@lcs-1
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 1. Click here for more information. 
,
@lcs-2
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 2. Click here for more information. 
,
@lcs-3
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 3. Click here for more information. 
,
@lcs-7
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 7. Click here for more information. 
,
@lcs-8
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 8. Click here for more information. 
,
@lcs-9
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 9. Click here for more information. 
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=../reference_structures/GGGTTAGGG/parallel_propeller_aaa-aaa.pdb

# metadynamics
The ERMSD action with label DIST1 calculates the following quantities:
 Quantity   
 Description  
DIST1.value
the eRMSD between the instantaneous structure and the reference structure that was inputmetad: 
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
=interD 
PACE
the frequency for hill addition
=250 
TAU
in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau
=70 
SIGMA
the widths of the Gaussian hills
=0.1 
FILE
 a file in which the list of added hills is stored
=HILLS 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=298 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=15 
GRID_MIN
the lower bounds for the grid
=0 
GRID_MAX
the upper bounds for the grid
=4.0 
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.02

# print 
The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.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
=tot_1,all_group_1.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=250 
FILE
the name of the file on which to output these quantities
=check_hbfix.dat
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=interD,DIST1,metad.bias 
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
=250