PLUMED-NEST

Project ID: plumID:23.031
Source: 1mfy/00-APO/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

# 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
The MOLINFO action with label  calculates somethingrna: 
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
The GROUP action with label rna calculates something
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 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 
REFERENCE
 this is the reference replica
# Add upper wall
The SHADOW action with label rmsd calculates the following quantities:
 Quantity   
 Description  
rmsd.value
the value of the shadow RMSDuws: 
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
The UPPER_WALLS action with label uws calculates something
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
=rmsd,uws.bias