PLUMED-NEST

Project ID: plumID:23.031
Source: 1anr/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
MOLINFOThis 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=conf_emin_PLUMED.pdb WHOLE The reference structure is whole, i
# Define RNA nucleic backbone
The MOLINFO action with label  calculates somethingrnaThe GROUP action with label rna calculates the following quantities:
 Quantity   
 Type   
 Description  
rna
atoms
indices of atoms specified in GROUP: GROUPDefine 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 ATOMSthe numerical indexes for the set of atoms in the group=1,2,5,6,33,36,37,40,41,67,70,71,74,75,98,101,102,105,106,131,134,135,138,139,165,168,169,172,173,198,201,202,205,206,228,231,232,235,236,259,262,263,266,267,289,292,293,296,297,323,326,327,330,331,356,359,360,363,364,390,393,394,397,398,421,424,425,428,429,452,455,456,459,460,482,485,486,489,490,516,519,520,523,524,550,553,554,557,558,584,587,588,591,592,617,620,621,624,625,651,654,655,658,659,682,685,686,689,690,712,715,716,719,720,743,746,747,750,751,773,776,777,780,781,804,807,808,811,812,834,837,838,841,842,868,871,872,875,876,899,902,903,906,907
# Reconstruct RNA PBC
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=rna EMST only for backward compatibility, as of PLUMED 2 STRIDE the frequency with which molecules are reassembled=1

# Define shadow RMSD on RNA backbone
rmsdThe SHADOW action with label rmsd calculates the following quantities:
 Quantity   
 Type   
 Description  
rmsd
scalar
the value of the shadow RMSD: SHADOWCommunicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation. More details ATOMSatoms for which we calculate the shadow RMSD=rna NOPBC ignore the periodic boundary conditions when calculating distances UPDATEstride for updating reference coordinates=100 REFERENCE this is the reference replica
# Add upper wall
uwsThe UPPER_WALLS action with label uws calculates the following quantities:
 Quantity   
 Type   
 Description  
uws.bias
scalar
the instantaneous value of the bias potential
uws.force2
scalar
the instantaneous value of the squared force due to this bias potential: 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=0.2 KAPPAthe force constant for the wall=10000.0 STRIDEthe frequency with which the forces due to the bias should be calculated=1

# Print useful info
PRINTPrint quantities to a file. More details FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=rmsd,uws.bias