Project ID: plumID:21.051
Source: plumed-nest/ST-MetaD/GAGA_gHBfix_1-0/plumed.0.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
tested onv2.9
tested onmaster
# vim:ft=plumed
Enables syntax highlighting for PLUMED files in vim. See here for more details.
# choose units - by default PLUMED uses kj/mol, nm, and ps # UNITS ENERGY=kcal/mol LENGTH=A
# UNTS !!!!!!!!!
# PDB that provides information on the molecules that are present in your system.
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
=GAGA_native.pdb
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
=1-263
#################################################################################################### # gHBfix RESTRAINT SECTION ####################################################################################################
group_nh_n:
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
=19,22,23,19,19,22,22,23,23,19,19,19,22,22,22,23,23,23,19,19,22,22,23,23,19,19,19,22,22,22,23,23,23,19,19,22,22,23,23,19,22,23,52,52,53,53,52,52,53,53,52,52,52,53,53,53,52,52,53,53,52,52,52,53,53,53,52,52,53,53,52,53,84,84,87,87,88,88,84,87,88,84,84,84,87,87,87,88,88,88,84,84,87,87,88,88,84,84,84,87,87,87,88,88,88,84,84,87,87,88,88,84,87,88,117,117,118,118,117,118,117,117,118,118,117,117,118,118,117,117,117,118,118,118,117,117,118,118,117,118,151,151,154,154,155,155,151,154,155,151,151,154,154,155,155,151,151,151,154,154,154,155,155,155,151,151,151,154,154,154,155,155,155,151,151,154,154,155,155,151,154,155,184,184,185,185,184,185,184,184,185,185,184,184,184,185,185,185,184,184,185,185,184,184,185,185,184,185,218,218,221,221,222,222,218,221,222,218,218,221,221,222,222,218,218,218,221,221,221,222,222,222,218,218,221,221,222,222,218,218,218,221,221,221,222,222,222,218,221,222,251,251,252,252,251,252,251,251,252,252,251,251,251,252,252,252,251,251,252,252,251,251,251,252,252,252,251,251,252,252
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=54,54,54,79,89,79,89,79,89,113,119,122,113,119,122,113,119,122,146,156,146,156,146,156,180,186,189,180,186,189,180,186,189,213,223,213,223,213,223,253,253,253,14,24,14,24,79,89,79,89,113,119,122,113,119,122,146,156,146,156,180,186,189,180,186,189,213,223,213,223,253,253,14,24,14,24,14,24,54,54,54,113,119,122,113,119,122,113,119,122,146,156,146,156,146,156,180,186,189,180,186,189,180,186,189,213,223,213,223,213,223,253,253,253,14,24,14,24,54,54,79,89,79,89,146,156,146,156,180,186,189,180,186,189,213,223,213,223,253,253,14,24,14,24,14,24,54,54,54,79,89,79,89,79,89,113,119,122,113,119,122,113,119,122,180,186,189,180,186,189,180,186,189,213,223,213,223,213,223,253,253,253,14,24,14,24,54,54,79,89,79,89,113,119,122,113,119,122,146,156,146,156,213,223,213,223,253,253,14,24,14,24,14,24,54,54,54,79,89,79,89,79,89,113,119,122,113,119,122,113,119,122,146,156,146,156,146,156,180,186,189,180,186,189,180,186,189,253,253,253,14,24,14,24,54,54,79,89,79,89,113,119,122,113,119,122,146,156,146,156,180,186,189,180,186,189,213,223,213,223
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={MATHEVAL FUNC=((-2092.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.3-x)+((-2092.0000000000)*(0.1)*(2*x-0.5))*step(x-0.3)+((2615.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.28-x)+((2615.0000000000)*(0.08)*(2*x-0.48))*step(x-0.28) R_0=1.0}
group_oh_nbo:
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
=31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,62,62,62,62,62,62,62,62,62,62,62,62,62,62,96,96,96,96,96,96,96,96,96,96,96,96,96,96,129,129,129,129,129,129,129,129,129,129,129,129,129,129,163,163,163,163,163,163,163,163,163,163,163,163,163,163,196,196,196,196,196,196,196,196,196,196,196,196,196,196,230,230,230,230,230,230,230,230,230,230,230,230,230,230,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=34,35,34,35,65,66,65,66,99,100,99,100,132,133,132,133,166,167,166,167,199,200,199,200,233,234,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,65,66,99,100,132,133,166,167,199,200,233,234,34,35,34,35,65,66,65,66,99,100,99,100,132,133,132,133,166,167,166,167,199,200,199,200,233,234,233,234
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={MATHEVAL FUNC=((-2092.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.3-x)+((-2092.0000000000)*(0.1)*(2*x-0.5))*step(x-0.3)+((2615.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.28-x)+((2615.0000000000)*(0.08)*(2*x-0.48))*step(x-0.28) R_0=1.0}
group_oh_bo:
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
=1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,31,1,1,31,1,62,62,62,62,62,62,62,62,62,62,62,62,62,96,96,96,96,96,96,96,96,96,96,96,96,96,129,129,129,129,129,129,129,129,129,129,129,129,129,163,163,163,163,163,163,163,163,163,163,163,163,163,196,196,196,196,196,196,196,196,196,196,196,196,196,230,230,230,230,230,230,230,230,230,230,230,230,230,261,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,261,263,263,261,263
GROUPB
Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)
=32,36,63,36,63,67,97,67,97,101,130,101,130,134,164,134,164,168,197,168,197,201,231,201,231,235,235,32,36,67,97,101,130,134,164,168,197,201,231,235,32,36,63,67,101,130,134,164,168,197,201,231,235,32,36,63,67,97,101,134,164,168,197,201,231,235,32,36,63,67,97,101,130,134,168,197,201,231,235,32,36,63,67,97,101,130,134,164,168,201,231,235,32,36,63,67,97,101,130,134,164,168,197,201,235,32,32,36,63,36,63,67,97,67,97,101,130,101,130,134,164,134,164,168,197,168,197,201,231,201,231,235,235
SWITCH
This keyword is used if you want to employ an alternative to the continuous switching function defined above
={MATHEVAL FUNC=((-2092.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.3-x)+((-2092.0000000000)*(0.1)*(2*x-0.5))*step(x-0.3)+((2615.0000000000)*(0.2-x)^2)*step(x-0.2)*step(0.28-x)+((2615.0000000000)*(0.08)*(2*x-0.48))*step(x-0.28) R_0=1.0}
tot_NH-N:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=group_nh_n
COEFFICIENTS
the coefficients of the arguments in your function
=1
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO tot_OH-nbO:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=group_oh_nbo
COEFFICIENTS
the coefficients 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 tot_OH-bO:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=group_oh_bo
COEFFICIENTS
the coefficients 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
tot:
COMBINE
Calculate a polynomial combination of a set of other variables. More details
ARG
the input to this function
=group_nh_n,group_oh_nbo,group_oh_bo
COEFFICIENTS
the coefficients of the arguments in your function
=1,-0.5,-0.5
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
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_NH-N
LABEL
a label for the action so that its output can be referenced in the input to other actions
=all_NH-N
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_OH-nbO
LABEL
a label for the action so that its output can be referenced in the input to other actions
=all_OH-nbO
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_OH-bO
LABEL
a label for the action so that its output can be referenced in the input to other actions
=all_OH-bO
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_NH-N,all_NH-N.bias,tot_OH-nbO,all_OH-nbO.bias,tot_OH-bO,all_OH-bO.bias,tot
STRIDE
the frequency with which the quantities of interest should be output
=1000
FILE
the name of the file on which to output these quantities
=check_HBfix.dat
# eRMSD with augmented cutoff, used for biasing. # The value of the cutoff determines at which distance a pair of nucleobases is counted # as a contact. An augmented value here allows forces to drive # the system towards and away from native even when nucleobases are far from # each other DIST0:
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-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information.
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information.
,
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. 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.
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=GAGA_native.pdb
CUTOFF
only pairs of atoms closer than CUTOFF are considered in the calculation
=3.2
# eRMSD with standard cutoff (2.4), used for monitoring only. # The cutoff employed here is the same used in the original paper # describing the eRMSD metric. This value allows only proper contact to # be included in the assessment of the structures. DIST1:
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-4
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 4. Click here for more information.
,
@lcs-5
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 5. Click here for more information.
,
@lcs-6
an ordered triplet of atoms on the 6-membered ring of the nucleobase in residue 6. 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.
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=GAGA_native.pdb
# metadynamics metad:
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
=DIST0
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
=4.5
GRID_SPACING
the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
=0.02 # print colvar 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
=DIST0,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