Project ID: plumID:22.013
Source: plumed/6e1u/production/plumed.production.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
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
=rna
res31:
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
=
@sugar-31
the heavy atoms of the sugar in residue 31. Click here for more information.
res23:
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
=
@sugar-23
the heavy atoms of the sugar in residue 23. Click here for more information.
res5:
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
=
@sugar-5
the heavy atoms of the sugar in residue 5. Click here for more information.

res31_l_C07_1070:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=res31,1070 res23_l_C11_1073:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=res23,1073 res5_l_C15_1064:
DISTANCE
Calculate the distance between a pair of atoms. More details
ATOMS
the pair of atom that we are calculating the distance between
=res5,1064
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
=res31_l_C07_1070,res23_l_C11_1073,res5_l_C15_1064
POWERS
the powers to which you are raising each of the arguments in your function
=1,1,1
COEFFICIENTS
the coefficients of the arguments in your function
=0.8368179798126221,-0.16150334477424622,-0.52311772108078
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
cn:
COORDINATIONNUMBER
Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of More details
SPECIESA
this keyword is used for colvars such as the coordination number
=1063-1099
SPECIESB
this keyword is used for colvars such as the coordination number
=1-1062
NN
The n parameter of the switching function
=4
R_0
The r_0 parameter of the switching function
=0.3
MAX
calculate the maximum value
={BETA=0.1}
MEAN
calculate the mean of all the quantities

rmsd1:
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
=PDB/rmsd1.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd2:
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
=PDB/rmsd2.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd3:
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
=PDB/rmsd3.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd4:
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
=PDB/rmsd4.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd5:
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
=PDB/rmsd5.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd6:
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
=PDB/rmsd6.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd7:
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
=PDB/rmsd7.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd8:
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
=PDB/rmsd8.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd9:
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
=PDB/rmsd9.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd10:
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
=PDB/rmsd10.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd11:
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
=PDB/rmsd11.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd12:
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
=PDB/rmsd12.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd13:
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
=PDB/rmsd13.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd14:
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
=PDB/rmsd14.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd15:
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
=PDB/rmsd15.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd16:
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
=PDB/rmsd16.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd17:
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
=PDB/rmsd17.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd18:
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
=PDB/rmsd18.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd19:
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
=PDB/rmsd19.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd20:
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
=PDB/rmsd20.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd21:
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
=PDB/rmsd21.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd22:
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
=PDB/rmsd22.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd23:
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
=PDB/rmsd23.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd24:
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
=PDB/rmsd24.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd25:
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
=PDB/rmsd25.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd26:
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
=PDB/rmsd26.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd27:
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
=PDB/rmsd27.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd28:
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
=PDB/rmsd28.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd29:
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
=PDB/rmsd29.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd30:
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
=PDB/rmsd30.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd31:
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
=PDB/rmsd31.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd32:
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
=PDB/rmsd32.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL rmsd33:
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
=PDB/rmsd33.pdb
TYPE
the manner in which RMSD alignment is performed
=OPTIMAL
COMMITTOR
Does a committor analysis. More details
...
ARG
the input for this action is the scalar output from one or more other actions
=cn.max
STRIDE
the frequency with which the CVs are analyzed
=500
BASIN_LL1
List of lower limits for basin #
=0.0
BASIN_UL1
List of upper limits for basin #
=1.0 ... COMMITTOR
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
SIGMA
the widths of the Gaussian hills
=0.06
HEIGHT
the heights of the Gaussian hills
=1.0
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=300.0
PACE
the frequency for hill addition
=2000
GRID_MIN
the lower bounds for the grid
=-3.79
GRID_MAX
the upper bounds for the grid
=3.60
GRID_BIN
the number of bins for the grid
=200
CALC_RCT
calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct]
... METAD
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=rmsd1,rmsd2,rmsd3,rmsd4,rmsd5,rmsd6,rmsd7,rmsd8,rmsd9,rmsd10,rmsd11,rmsd12,rmsd13,rmsd14,rmsd15,rmsd16,rmsd17,rmsd18,rmsd19,rmsd20,rmsd21,rmsd22,rmsd23,rmsd24,rmsd25,rmsd26,rmsd27,rmsd28,rmsd29,rmsd30,rmsd31,rmsd32,rmsd33
STRIDE
the frequency with which the quantities of interest should be output
=10
FILE
the name of the file on which to output these quantities
=6e1u_rmsd
PRINT
Print quantities to a file. More details
ARG
the input for this action is the scalar output from one or more other actions
=res31_l_C07_1070,res23_l_C11_1073,res5_l_C15_1064,cn.max,cn.mean,rc1,metad.bias,metad.rbias
STRIDE
the frequency with which the quantities of interest should be output
=10
FILE
the name of the file on which to output these quantities
=6e1u_COLVAR