PLUMED-NEST

Project ID: plumID:20.007
Source: single/plumed.dat
Originally used with PLUMED version: 2.4.2
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

# The commented out lines are the original implementation. They have been altered to be compatible with newer PLUMED versions.

RESTART
Activate restart. 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.pdb 
MOLTYPE
 what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible
=protein
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
=1-2604  
rmsd: 
RMSD
Calculate the RMSD with respect to a reference structure. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=rmsd.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL

d-r28_l110: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-28
the CA atom in residue 28. Click here for more information. 
,
@CA-110
the CA atom in residue 110. Click here for more information. 
The DISTANCE action with label d-r28_l110 calculates a scalar quantityd-l110_l118: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-110
the CA atom in residue 110. Click here for more information. 
,
@CA-118
the CA atom in residue 118. Click here for more information. 
The DISTANCE action with label d-l110_l118 calculates a scalar quantityd-r85_l112: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-85
the CA atom in residue 85. Click here for more information. 
,
@CA-112
the CA atom in residue 112. Click here for more information. 
The DISTANCE action with label d-r85_l112 calculates a scalar quantityd-r157_l116: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-157
the CA atom in residue 157. Click here for more information. 
,
@CA-116
the CA atom in residue 116. Click here for more information. 
The DISTANCE action with label d-r157_l116 calculates a scalar quantityd-r25_l115: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-25
the CA atom in residue 25. Click here for more information. 
,
@CA-115
the CA atom in residue 115. Click here for more information. 
The DISTANCE action with label d-r25_l115 calculates a scalar quantityd-l111_l112: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-111
the CA atom in residue 111. Click here for more information. 
,
@CA-112
the CA atom in residue 112. Click here for more information. 
The DISTANCE action with label d-l111_l112 calculates a scalar quantityd-r97_l115: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-97
the CA atom in residue 97. Click here for more information. 
,
@CA-115
the CA atom in residue 115. Click here for more information. 
The DISTANCE action with label d-r97_l115 calculates a scalar quantityd-r142_l119: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-142
the CA atom in residue 142. Click here for more information. 
,
@CA-119
the CA atom in residue 119. Click here for more information. 
The DISTANCE action with label d-r142_l119 calculates a scalar quantityd-r154_l113: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-154
the CA atom in residue 154. Click here for more information. 
,
@CA-113
the CA atom in residue 113. Click here for more information. 
The DISTANCE action with label d-r154_l113 calculates a scalar quantityd-r67_l116: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-67
the CA atom in residue 67. Click here for more information. 
,
@CA-116
the CA atom in residue 116. Click here for more information. 
The DISTANCE action with label d-r67_l116 calculates a scalar quantityd-r43_l114: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-43
the CA atom in residue 43. Click here for more information. 
,
@CA-114
the CA atom in residue 114. Click here for more information. 
The DISTANCE action with label d-r43_l114 calculates a scalar quantityd-r34_l114: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-34
the CA atom in residue 34. Click here for more information. 
,
@CA-114
the CA atom in residue 114. Click here for more information. 
The DISTANCE action with label d-r34_l114 calculates a scalar quantityd-r34_l118: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-34
the CA atom in residue 34. Click here for more information. 
,
@CA-118
the CA atom in residue 118. Click here for more information. 
The DISTANCE action with label d-r34_l118 calculates a scalar quantityd-l112_l113: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-112
the CA atom in residue 112. Click here for more information. 
,
@CA-113
the CA atom in residue 113. Click here for more information. 
The DISTANCE action with label d-l112_l113 calculates a scalar quantityd-r49_l116: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-49
the CA atom in residue 49. Click here for more information. 
,
@CA-116
the CA atom in residue 116. Click here for more information. 
The DISTANCE action with label d-r49_l116 calculates a scalar quantityd-l115_l116: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=
@CA-115
the CA atom in residue 115. Click here for more information. 
,
@CA-116
the CA atom in residue 116. Click here for more information. 

The DISTANCE action with label d-l115_l116 calculates a scalar quantityd1769_1819: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=1769,1819
The DISTANCE action with label d1769_1819 calculates a scalar quantitypsi_114_1: 
TORSION
Calculate a torsional angle. More details
 
ATOMS
the four atoms involved in the torsional angle
=1770,1772,1788,1790


The TORSION action with label psi_114_1 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
=d-r28_l110,d-l110_l118,d-r85_l112,d-r157_l116,d-r25_l115,d-l111_l112,d-r97_l115,d-r142_l119,d-r154_l113,d-r67_l116,d-r43_l114,d-r34_l114,d-r34_l118,d-l112_l113,d-r49_l116,d-l115_l116
COEFFICIENTS
 the coefficients of the arguments in your function
=5.690912902355194092e-02,-1.696033775806427002e-01,-1.088943518698215485e-02,-3.811309486627578735e-02,-3.845035657286643982e-02,-3.398763835430145264e-01,6.818664073944091797e-01,1.402324438095092773e-01,5.613043904304504395e-02,1.617383360862731934e-01,8.190712332725524902e-02,-2.790833413600921631e-01,4.563379585742950439e-01,1.509449779987335205e-01,4.242382943630218506e-02,-1.344945281744003296e-01 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE



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
=rc2 
ARG
the input to this function
=d-r28_l110,d-l110_l118,d-r85_l112,d-r157_l116,d-r25_l115,d-l111_l112,d-r97_l115,d-r142_l119,d-r154_l113,d-r67_l116,d-r43_l114,d-r34_l114,d-r34_l118,d-l112_l113,d-r49_l116,d-l115_l116
COEFFICIENTS
 the coefficients of the arguments in your function
=-1.883340626955032349e-01,4.097261726856231689e-01,1.357467919588088989e-01,4.463798403739929199e-01,-1.859887838363647461e-01,2.378992550075054169e-02,-3.209500312805175781e-01,4.577260613441467285e-01,1.797014027833938599e-01,3.510920107364654541e-01,-1.946701705455780029e-01,-2.567137824371457100e-03,1.762732118368148804e-01,-7.985947653651237488e-03,-7.434802502393722534e-02,-3.417430073022842407e-02 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
... COMBINE


METAD
Used to performed metadynamics on one or more collective variables. More details
 ...
LABEL
a label for the action so that its output can be referenced in the input to other actions
=metad
ARG
the input for this action is the scalar output from one or more other actions
=rc1,rc2
PACE
the frequency for hill addition
=500
HEIGHT
the heights of the Gaussian hills
=1.5
SIGMA
the widths of the Gaussian hills
=0.05,0.05
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10.0
#GRID_MIN=1.00,0.21
#GRID_MAX=5.50,4.70
#GRID_BIN=300,300
#REWEIGHTING_NGRID=300,300
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
... METAD


The METAD action with label metad calculates the following quantities:
 Quantity   
 Description  
metad.bias
the instantaneous value of the bias potential
UPPER_WALLS
Defines a wall for the value of one or more collective variables, More details
 
ARG
the arguments on which the bias is acting
=rmsd 
AT
the positions of the wall
=0.5 
KAPPA
the force constant for the wall
=1000.0 
EXP
 the powers for the walls
=4 
EPS
 the values for s_i in the expression for a wall
=1 
OFFSET
 the offset for the start of the wall
=0 
LABEL
a label for the action so that its output can be referenced in the input to other actions
=uwall


#PRINT ARG=d-r28_l110,d-l110_l118,d-r85_l112,d-r157_l116,d-r25_l115,d-l111_l112,d-r97_l115,d-r142_l119,d-r154_l113,d-r67_l116,d-r43_l114,d-r34_l114,d-r34_l118,d-l112_l113,d-r49_l116,d-l115_l116,rc1,rc2,uwall.bias,metad.bias,metad.rbias STRIDE=1 FILE=COLVAR
#PRINT ARG=d1769_1819,psi_114_1,rmsd,uwall.bias,metad.bias,metad.rbias STRIDE=50 FILE=COLVAR_strucutre

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d-r28_l110,d-l110_l118,d-r85_l112,d-r157_l116,d-r25_l115,d-l111_l112,d-r97_l115,d-r142_l119,d-r154_l113,d-r67_l116,d-r43_l114,d-r34_l114,d-r34_l118,d-l112_l113,d-r49_l116,d-l115_l116,rc1,rc2,uwall.bias,metad.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
=COLVAR
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=d1769_1819,psi_114_1,rmsd,uwall.bias,metad.bias 
STRIDE
 the frequency with which the quantities of interest should be output
=50 
FILE
the name of the file on which to output these quantities
=COLVAR_strucutre