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
# Reference PDBMOLINFOThis command is used to provide information on the molecules that are present in your system. More detailsSTRUCTURE=conf_emin_PLUMED.pdba file in pdb format containing a reference structureWHOLE# Define RNA nucleic backbone rna:The reference structure is whole, iGROUPDefine 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 detailsATOMS=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 PBCthe numerical indexes for the set of atoms in the groupWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More detailsENTITY0=rnathe atoms that make up a molecule that you wish to alignEMSTDefine atoms sequence in entities using an Euclidean minimum spanning treeSTRIDE=1the frequency with which molecules are reassembled
# Define shadow RMSD on RNA backbone rmsd:SHADOWCommunicate atoms positions among replicas and calculate the RMSD with respect to a mother (reference) simulation. More detailsATOMS=rnaatoms for which we calculate the shadow RMSDNOPBCignore the periodic boundary conditions when calculating distancesUPDATE=100stride for updating reference coordinatesREFERENCE# Add upper wall uws:this is the reference replicaUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=rmsdthe arguments on which the bias is actingAT=0.2the positions of the wallKAPPA=10000.0the force constant for the wallSTRIDE=1the frequency with which the forces due to the bias should be calculated
# Print useful infoPrint quantities to a file. More detailsFILE=COLVARthe name of the file on which to output these quantitiesSTRIDE=500the frequency with which the quantities of interest should be outputARG=rmsd,uws.biasthe input for this action is the scalar output from one or more other actions