Project ID: plumID:23.031
Source: 1mfy/01-BENX/2-Production/plumed.dat
Originally used with PLUMED version: 2.10
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
# Reference PDB

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
=conf_emin_PLUMED.pdb 
WHOLE
 The reference structure is whole, i

# Define RNA nucleic backbone
rna: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1,2,5,6,32,35,36,39,40,66,69,70,73,74,96,99,100,103,104,129,132,133,136,137,163,166,167,170,171,196,199,200,203,204,229,232,233,236,237,262,265,266,269,270,293,296,297,300,301,326,329,330,333,334,359,362,363,366,367,393,396,397,400,401,427,430,431,434,435,458,461,462,465,466,488,491,492,495,496,518,521,522,525,526,549,552,553,556,557,583,586,587,590,591,617,620,621,624,625,648,651,652,655,656,679,682,683,686,687,709,712,713,716,717,743,746,747,750,751,774,777,778,781,782,804,807,808,811,812,834,837,838,841,842,864,867,868,871,872,895,898,899,902,903,929,932,933,936,937,960,963,964,967,968
# Reconstruct RNA PBC

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
=rna 
EMST
 Define atoms sequence in entities using an Euclidean minimum spanning tree
 
STRIDE
 the frequency with which molecules are reassembled
=1
# Define probe
probe: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=991,992,993,994,995,996
# Wrap probe around RNA

WRAPAROUND
Rebuild periodic boundary conditions around chosen atoms. More details
 
ATOMS
wrapped atoms
=probe 
AROUND
reference atoms
=rna 
GROUPBY
 group atoms so as not to break molecules
=6 
STRIDE
 the frequency with which molecules are reassembled
=1

# Align system to RNA nucleic backbone

FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=conf_emin_PLUMED.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
STRIDE
 the frequency with which molecules are reassembled
=1

# Define probe center
com: 
CENTER
Calculate the center for a group of atoms, with arbitrary weights. More details
 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=probe 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# Calculate position
pos: 
POSITION
Calculate the components of the position of an atom. More details
 
ATOM
the atom number
=com 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# Do Metadynamics
mtd: 
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
=pos.x,pos.y,pos.z 
SIGMA
the widths of the Gaussian hills
=0.1,0.1,0.1 
HEIGHT
the heights of the Gaussian hills
=1.20 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=10 
PACE
the frequency for hill addition
=500 
STRIDE
the frequency with which the forces due to the bias should be calculated
=1

GRID_MIN
the lower bounds for the grid
=-3.806067,-4.175067,-4.002067 
GRID_MAX
the upper bounds for the grid
=11.209067,8.304067,8.001067 
FILE
 a file in which the list of added hills is stored
=HILLS
...

# Minimum distance probe COM-RNA
dist: 
DISTANCES
Calculate the distances between multiple piars of atoms More details
 
GROUPA
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=com 
GROUPB
Calculate the distances between all the atoms in GROUPA and all the atoms in GROUPB
=rna 
MIN
calculate the minimum value
={BETA=50.} 
NOPBC
 ignore the periodic boundary conditions when calculating distances

# Upper wall
uwd: 
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
=dist.min 
AT
the positions of the wall
=1.0 
KAPPA
the force constant for the wall
=10000.0 
STRIDE
the frequency with which the forces due to the bias should be calculated
=1

# Define shadow RMSD on RNA backbone
rmsd: 
SHADOW
Communicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation. More details
 
ATOMS
atoms for which we calculate the shadow RMSD
=rna 
NOPBC
 ignore the periodic boundary conditions when calculating distances
 
UPDATE
stride for updating reference coordinates
=100
# Add upper wall
uws: 
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
=0.2 
KAPPA
the force constant for the wall
=10000.0 
STRIDE
the frequency with which the forces due to the bias should be calculated
=1

# Print useful info

PRINT
Print quantities to a file. More details
 
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
=500 
ARG
the input for this action is the scalar output from one or more other actions
=pos.x,pos.y,pos.z,dist.min,rmsd,mtd.bias,uwd.bias,uws.bias