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.

RESTARTActivate restart. More details

The RESTART action with label  calculates somethingMOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa 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
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-2604  
rmsdThe RMSD action with label rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd
scalar
the RMSD between the instantaneous structure and the reference structure that was input: RMSDCalculate the RMSD with respect to a reference structure. This action has hidden defaults. More details REFERENCEa 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
rmsd: RMSDCalculate the RMSD with respect to a reference structure. This action uses the defaults shown here. More details REFERENCEa 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  NUMBER if there are multiple structures in the pdb file you can specify that you want the RMSD from a specific structure by specifying its place in the file here=0

d-r28_l110The DISTANCE action with label d-r28_l110 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r28_l110
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-28the CA atom in residue 28. Click here for more information. ,@CA-110the CA atom in residue 110. Click here for more information. 
d-l110_l118The DISTANCE action with label d-l110_l118 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-l110_l118
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-110the CA atom in residue 110. Click here for more information. ,@CA-118the CA atom in residue 118. Click here for more information. 
d-r85_l112The DISTANCE action with label d-r85_l112 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r85_l112
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-85the CA atom in residue 85. Click here for more information. ,@CA-112the CA atom in residue 112. Click here for more information. 
d-r157_l116The DISTANCE action with label d-r157_l116 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r157_l116
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-157the CA atom in residue 157. Click here for more information. ,@CA-116the CA atom in residue 116. Click here for more information. 
d-r25_l115The DISTANCE action with label d-r25_l115 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r25_l115
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-25the CA atom in residue 25. Click here for more information. ,@CA-115the CA atom in residue 115. Click here for more information. 
d-l111_l112The DISTANCE action with label d-l111_l112 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-l111_l112
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-111the CA atom in residue 111. Click here for more information. ,@CA-112the CA atom in residue 112. Click here for more information. 
d-r97_l115The DISTANCE action with label d-r97_l115 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r97_l115
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-97the CA atom in residue 97. Click here for more information. ,@CA-115the CA atom in residue 115. Click here for more information. 
d-r142_l119The DISTANCE action with label d-r142_l119 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r142_l119
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-142the CA atom in residue 142. Click here for more information. ,@CA-119the CA atom in residue 119. Click here for more information. 
d-r154_l113The DISTANCE action with label d-r154_l113 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r154_l113
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-154the CA atom in residue 154. Click here for more information. ,@CA-113the CA atom in residue 113. Click here for more information. 
d-r67_l116The DISTANCE action with label d-r67_l116 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r67_l116
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-67the CA atom in residue 67. Click here for more information. ,@CA-116the CA atom in residue 116. Click here for more information. 
d-r43_l114The DISTANCE action with label d-r43_l114 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r43_l114
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-43the CA atom in residue 43. Click here for more information. ,@CA-114the CA atom in residue 114. Click here for more information. 
d-r34_l114The DISTANCE action with label d-r34_l114 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r34_l114
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-34the CA atom in residue 34. Click here for more information. ,@CA-114the CA atom in residue 114. Click here for more information. 
d-r34_l118The DISTANCE action with label d-r34_l118 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r34_l118
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-34the CA atom in residue 34. Click here for more information. ,@CA-118the CA atom in residue 118. Click here for more information. 
d-l112_l113The DISTANCE action with label d-l112_l113 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-l112_l113
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-112the CA atom in residue 112. Click here for more information. ,@CA-113the CA atom in residue 113. Click here for more information. 
d-r49_l116The DISTANCE action with label d-r49_l116 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-r49_l116
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-49the CA atom in residue 49. Click here for more information. ,@CA-116the CA atom in residue 116. Click here for more information. 
d-l115_l116The DISTANCE action with label d-l115_l116 calculates the following quantities:
 Quantity   
 Type   
 Description  
d-l115_l116
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=@CA-115the CA atom in residue 115. Click here for more information. ,@CA-116the CA atom in residue 116. Click here for more information. 

d1769_1819The DISTANCE action with label d1769_1819 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1769_1819
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1769,1819
psi_114_1The TORSION action with label psi_114_1 calculates the following quantities:
 Quantity   
 Type   
 Description  
psi_114_1
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=1770,1772,1788,1790


COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=rc1The COMBINE action with label rc1 calculates the following quantities:
 Quantity   
 Type   
 Description  
rc1
scalar
a linear compbination ARGthe values 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 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE



COMBINECalculate a polynomial combination of a set of other variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=rc2The COMBINE action with label rc2 calculates the following quantities:
 Quantity   
 Type   
 Description  
rc2
scalar
a linear compbination ARGthe values 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 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
... COMBINE


METADUsed to performed metadynamics on one or more collective variables. This action has hidden defaults. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
ARGthe labels of the scalars on which the bias will act=rc1,rc2
PACEthe frequency for hill addition=500
HEIGHTthe heights of the Gaussian hills=1.5
SIGMAthe widths of the Gaussian hills=0.05,0.05
BIASFACTORuse 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
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
... METAD
METADUsed to performed metadynamics on one or more collective variables. This action uses the defaults shown here. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metad
ARGthe labels of the scalars on which the bias will act=rc1,rc2
PACEthe frequency for hill addition=500
HEIGHTthe heights of the Gaussian hills=1.5
SIGMAthe widths of the Gaussian hills=0.05,0.05
BIASFACTORuse 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
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=300.0
 FILE a file in which the list of added hills is stored=HILLS
... METAD


UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=rmsd ATthe positions of the wall=0.5 KAPPAthe 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 LABELa label for the action so that its output can be referenced in the input to other actions=uwallThe UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Type   
 Description  
uwall.bias
scalar
the instantaneous value of the bias potential
uwall.force2
scalar
the instantaneous value of the squared force due to this bias potential


#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

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=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 FILEthe name of the file on which to output these quantities=COLVAR
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1769_1819,psi_114_1,rmsd,uwall.bias,metad.bias STRIDE the frequency with which the quantities of interest should be output=50 FILEthe name of the file on which to output these quantities=COLVAR_strucutre