PLUMED-NEST

Project ID: plumID:23.031
Source: 1mfy/06-BENF/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=1,2,5,6,32,35,36,39,40,66,69,70,73,74,96,99,100,103,104,129,132,133,136,137,163,166,167,170,171,196,199,200,203,204,229,232,233,236,237,262,265,266,269,270,293,296,297,300,301,326,329,330,333,334,359,362,363,366,367,393,396,397,400,401,427,430,431,434,435,458,461,462,465,466,488,491,492,495,496,518,521,522,525,526,549,552,553,556,557,583,586,587,590,591,617,620,621,624,625,648,651,652,655,656,679,682,683,686,687,709,712,713,716,717,743,746,747,750,751,774,777,778,781,782,804,807,808,811,812,834,837,838,841,842,864,867,868,871,872,895,898,899,902,903,929,932,933,936,937,960,963,964,967,968
# Reconstruct RNA PBC
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 probe
probeThe GROUP action with label probe calculates the following quantities:
 Quantity   
 Type   
 Description  
probe
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=991,992,993,994,995,996,997,998,999,1000,1001,1002,1003,1004,1005,1006,1007,1008,1009,1010
# Wrap probe around RNA
WRAPAROUNDRebuild periodic boundary conditions around chosen atoms. More details ATOMSwrapped atoms=probe AROUNDreference atoms=rna GROUPBY group atoms so as not to break molecules=20 STRIDE the frequency with which molecules are reassembled=1

# Align system to RNA nucleic backbone
FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details REFERENCEa 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
comThe CENTER_FAST action with label com calculates the following quantities:
 Quantity   
 Type   
 Description  
com
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=probe NOPBC ignore the periodic boundary conditions when calculating distances
# Calculate position
posThe POSITION action with label pos calculates the following quantities:
 Quantity   
 Type   
 Description  
pos.x
scalar
the x-component of the atom position
pos.y
scalar
the y-component of the atom position
pos.z
scalar
the z-component of the atom position: POSITIONCalculate the components of the position of an atom or atoms. More details ATOMthe atom number=com NOPBC ignore the periodic boundary conditions when calculating distances
# Do Metadynamics
mtdThe METAD action with label mtd calculates the following quantities:
 Quantity   
 Type   
 Description  
mtd.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ...
ARGthe labels of the scalars on which the bias will act=pos.x,pos.y,pos.z SIGMAthe widths of the Gaussian hills=0.1,0.1,0.1 HEIGHTthe heights of the Gaussian hills=1.20 BIASFACTORuse well tempered metadynamics and use this bias factor=10 PACEthe frequency for hill addition=500 STRIDEthe frequency with which the forces due to the bias should be calculated=1
GRID_MINthe lower bounds for the grid=-3.729067,-4.133067,-3.998067 GRID_MAXthe upper bounds for the grid=11.233068,8.309067,8.004066 FILE a file in which the list of added hills is stored=HILLS
...

# Minimum distance probe COM-RNA
distThe DISTANCES action with label dist calculates the following quantities:
 Quantity   
 Type   
 Description  
dist
vector
the DISTANCES between the each pair of atoms that were specified
dist_min
scalar
the minimum colvar: DISTANCESCalculate the distances between multiple piars of atoms This action is a shortcut. More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=com GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=rna MINcalculate the minimum value={BETA=50.} NOPBC ignore the periodic boundary conditions when calculating distances
# PLUMED interprets the command:
# dist: DISTANCES GROUPA=com GROUPB=rna MIN={BETA=50.} NOPBC
# as follows (Click the red comment above to revert to the short version of the input):
distThe DISTANCE action with label dist calculates the following quantities:
 Quantity   
 Type   
 Description  
dist
vector
the DISTANCE for each set of specified atoms: DISTANCECalculate the distance/s between pairs of atoms. More details NOPBC ignore the periodic boundary conditions when calculating distances ATOMS1the pair of atom that we are calculating the distance between=com,1 ATOMS2the pair of atom that we are calculating the distance between=com,2 ATOMS3the pair of atom that we are calculating the distance between=com,5 ATOMS4the pair of atom that we are calculating the distance between=com,6 ATOMS5the pair of atom that we are calculating the distance between=com,32     # Action input conctinues with 149 further ATOMSn keywords, 
dist_me_minThe CUSTOM action with label dist_me_min calculates the following quantities:
 Quantity   
 Type   
 Description  
dist_me_min
vector
the vector obtained by doing an element-wise application of an arbitrary function to the input vectors: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dist FUNCthe function you wish to evaluate=exp(50./x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dist_mec_minThe SUM action with label dist_mec_min calculates the following quantities:
 Quantity   
 Type   
 Description  
dist_mec_min
scalar
the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=dist_me_min PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
dist_minThe CUSTOM action with label dist_min calculates the following quantities:
 Quantity   
 Type   
 Description  
dist_min
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dist_mec_min FUNCthe function you wish to evaluate=50./log(x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- # Upper wall
uwdThe UPPER_WALLS action with label uwd calculates the following quantities:
 Quantity   
 Type   
 Description  
uwd.bias
scalar
the instantaneous value of the bias potential
uwd.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=dist.min ATthe positions of the wall=1.0 KAPPAthe force constant for the wall=10000.0 STRIDEthe frequency with which the forces due to the bias should be calculated=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
# 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=pos.x,pos.y,pos.z,dist.min,rmsd,mtd.bias,uwd.bias,uws.bias