Project ID: plumID:23.031
Source: 1mfy/05-MEPY/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=1,2,5,6,32,35,36,39,40,66,69,70,73,74,96,99,100,103,104,129,132,133,136,137,163,166,167,170,171,196,199,200,203,204,229,232,233,236,237,262,265,266,269,270,293,296,297,300,301,326,329,330,333,334,359,362,363,366,367,393,396,397,400,401,427,430,431,434,435,458,461,462,465,466,488,491,492,495,496,518,521,522,525,526,549,552,553,556,557,583,586,587,590,591,617,620,621,624,625,648,651,652,655,656,679,682,683,686,687,709,712,713,716,717,743,746,747,750,751,774,777,778,781,782,804,807,808,811,812,834,837,838,841,842,864,867,868,871,872,895,898,899,902,903,929,932,933,936,937,960,963,964,967,968 # Reconstruct RNA 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=1 # Define probe probe:the frequency with which molecules are reassembledGROUPDefine 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=991,992,993,994,995,996,997 # Wrap probe around RNAthe numerical indexes for the set of atoms in the groupWRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More detailsATOMS=probewrapped atomsAROUND=rnareference atomsGROUPBY=7group atoms so as not to break moleculesSTRIDE=1the frequency with which molecules are reassembled
# Align system to RNA nucleic backboneFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More detailsREFERENCE=conf_emin_PLUMED.pdba file in pdb format containing the reference structure and the atoms involved in the CVTYPE=OPTIMALthe manner in which RMSD alignment is performedNOPBCignore the periodic boundary conditions when calculating distancesSTRIDE=1the frequency with which molecules are reassembled
# Define probe center com:CENTERCalculate the center for a group of atoms, with arbitrary weights. More detailsATOMS=probethe group of atoms that you are calculating the Gyration Tensor forNOPBC# Calculate position pos:ignore the periodic boundary conditions when calculating distancesPOSITIONCalculate the components of the position of an atom. More detailsATOM=comthe atom numberNOPBC# Do Metadynamics mtd:ignore the periodic boundary conditions when calculating distancesMETAD...Used to performed metadynamics on one or more collective variables. More detailsARG=pos.x,pos.y,pos.zthe input for this action is the scalar output from one or more other actionsSIGMA=0.1,0.1,0.1the widths of the Gaussian hillsHEIGHT=1.20the heights of the Gaussian hillsBIASFACTOR=10use well tempered metadynamics and use this bias factorPACE=500the frequency for hill additionSTRIDE=1the frequency with which the forces due to the bias should be calculatedGRID_MIN=-3.877620,-4.193620,-4.049621the lower bounds for the gridGRID_MAX=11.244620,8.352620,8.048621the upper bounds for the gridFILE=HILLS ...a file in which the list of added hills is stored
# Minimum distance probe COM-RNA dist:DISTANCESCalculate the distances between multiple piars of atoms More detailsGROUPA=comCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBGROUPB=rnaCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPBMIN={BETA=50.}calculate the minimum valueNOPBC# Upper wall uwd:ignore the periodic boundary conditions when calculating distancesUPPER_WALLSDefines a wall for the value of one or more collective variables, More detailsARG=dist.minthe arguments on which the bias is actingAT=1.0the positions of the wallKAPPA=10000.0the force constant for the wallSTRIDE=1the frequency with which the forces due to the bias should be calculated
# 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=100 # Add upper wall uws:stride for updating reference coordinatesUPPER_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=pos.x,pos.y,pos.z,dist.min,rmsd,mtd.bias,uwd.bias,uws.biasthe input for this action is the scalar output from one or more other actions