PLUMED-NEST

Project ID: plumID:20.033
Source: PRODUCTION/plumed.dat
Originally used with PLUMED version: 2.6
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

#RESTART

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=structure.pdb
# define all heavy atoms using GROMACS index file

The MOLINFO action with label  calculates somethingprotein-h: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H
The GROUP action with label protein-h calculates somethingprotein: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein
The GROUP action with label protein calculates somethingProtein-noASPGLU-noH: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=Protein-H_&_!GLU_ASP_&_OE1_OE2_OD1_OD2
The GROUP action with label Protein-noASPGLU-noH calculates somethingsystem: 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 NDX_FILEthe name of index file (gromacs syntax)=index.ndx NDX_GROUPthe name of the group to be imported (gromacs syntax) - first group found is used by default=System
# make protein whole: add reference position of first heavy atom (in nm)
The GROUP action with label system calculates somethingWHOLEMOLECULESThis 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=1-19086 ENTITY1the atoms that make up a molecule that you wish to align=19087-38172 ENTITY2the atoms that make up a molecule that you wish to align=38173-57258 ADDREFERENCE Define the reference position of the first atom of each entity using a PDB file REF0=16.995,21.964,24.520 REF1=26.253,18.440,24.5030 REF2=24.616,28.069,24.203

RMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=6vxx_1_1_1_aligned_struct_RBD_renumbered.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL LABELa label for the action so that its output can be referenced in the input to other actions=rmsd_closed_charmm_6vxx
The RMSD action with label rmsd_closed_charmm_6vxx calculates the following quantities:
 Quantity   
 Description  
rmsd_closed_charmm_6vxx.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputRMSDCalculate the RMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=rmsd_structure_no487496.pdb TYPE the manner in which RMSD alignment is performed=OPTIMAL LABELa label for the action so that its output can be referenced in the input to other actions=rmsd_open

The RMSD action with label rmsd_open calculates the following quantities:
 Quantity   
 Description  
rmsd_open.value
the RMSD distance between the instaneous structure and the reference structure/s that were inputgly234NTFdown:  DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=3316,3318,3320,3323,3324,3325,3327,3328,17553,17555,17556,17558,17561,17563,17565,17567,17569,17571,17573,17574,17575,17579,17580,17582,17583,17585,17588,17590,17592,17594,17596,17598,17600,17601,17602,17606,17607,17609,17610,17612,17615,17616,17618,17620,17622,17624,17626,17627,17629,17631,17633,17635,17637,17640,17642,17643,17645,17647,17649,17651,17653,17655,17657,17659,17662,17664,17665,17667,17669 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=43296,43298,43300,43303,43304,43306,43308,43309,43311,43313,43315,43316,43317,43319,43321,43325,43326,44813,44815,44817,44820,44821,44822,44825,44826,44827,44829,44831,44834,44835,44837,44839,44840,44842,44844,44846,44847,44848,44850,44852,44855,44857,44861,44865,44866,44951,44953,44955,44958,44961,44964,44966,44967,44970,44973,44974,45041,45043,45045,45048,45051,45054,45057,45061,45062,45097,45099,45101,45104,45107,45108,45109,45110,45111,45112,45114,45116,45119,45122,45125,45127,45128,45131,45134,45135,45136,45138,45140,45143,45144,45145,45146,45147,45148,45150,45152,45154,45158,45161,45165,45166,45178,45180,45182,45184,45188,45190,45191,45192,45194,45196,45199,45202,45203,45204,45205,45206,45247,45249,45251,45254,45257,45258,45259,45262,45263 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.32 NN=6 MM=12}


The DISTANCES action with label gly234NTFdown calculates the following quantities:
 Quantity   
 Description  
gly234NTFdown.lessthan
the number of colvars that have a value less than a threshold
gly234NTFdown.value
the DISTANCES between the each pair of atoms that were specifiedgly165NTF_up:  DISTANCESCalculate the distances between multiple piars of atoms More details GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=2196,2198,2200,2203,2204,2205,2207,2208,17435,17437,17438,17440,17443,17445,17447,17449,17451,17453,17455,17456,17457,17461,17462,17464,17465,17467,17470,17472,17474,17476,17478,17480,17482,17483,17484,17488,17489,17491,17492,17494,17497,17498,17500,17502,17504,17506,17508,17509,17511,17513,17515,17517,17519,17522,17524,17525,17527,17529,17531,17533,17535,17537,17539,17541,17544,17546,17547,17549,17551 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB=43296,43298,43300,43303,43304,43306,43308,43309,43311,43313,43315,43316,43317,43319,43321,43325,43326,44813,44815,44817,44820,44821,44822,44825,44826,44827,44829,44831,44834,44835,44837,44839,44840,44842,44844,44846,44847,44848,44850,44852,44855,44857,44861,44865,44866,44951,44953,44955,44958,44961,44964,44966,44967,44970,44973,44974,45041,45043,45045,45048,45051,45054,45057,45061,45062,45097,45099,45101,45104,45107,45108,45109,45110,45111,45112,45114,45116,45119,45122,45125,45127,45128,45131,45134,45135,45136,45138,45140,45143,45144,45145,45146,45147,45148,45150,45152,45154,45158,45161,45165,45166,45178,45180,45182,45184,45188,45190,45191,45192,45194,45196,45199,45202,45203,45204,45205,45206,45247,45249,45251,45254,45257,45258,45259,45262,45263 LESS_THANcalculate the number of variables that are less than a certain target value. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.32 NN=6 MM=12}

# create EMMI score
The DISTANCES action with label gly165NTF_up calculates the following quantities:
 Quantity   
 Description  
gly165NTF_up.lessthan
the number of colvars that have a value less than a threshold
gly165NTF_up.value
the DISTANCES between the each pair of atoms that were specifiedEMMICalculate the fit of a structure or ensemble of structures with a cryo-EM density map. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=gmm NOPBC ignore the periodic boundary conditions when calculating distances TEMPtemperature=310.0 NL_STRIDEThe frequency with which we are updating the neighbor list=100 NL_CUTOFFThe cutoff in overlap for the neighbor list=0.01
ATOMSatoms for which we calculate the density map, typically all heavy atoms=Protein-noASPGLU-noH GMM_FILEfile with the parameters of the GMM components=SARS_COV2.dat
SIGMA_MINminimum uncertainty=0.05 RESOLUTIONCryo-EM map resolution=0.1 NOISETYPEfunctional form of the noise (GAUSS, OUTLIERS, MARGINAL)=MARGINAL
#WRITE_OV=OV_FILE.dat 
#WRITE_OV_STRIDE=500
...

# translate into bias
The EMMI action with label gmm calculates the following quantities:
 Quantity   
 Description  
gmm.scoreb
Bayesian score
gmm.acc
MC acceptance for uncertainty
gmm.sigma
uncertainty in the forward models and experiment
gmm.neff
effective number of replicasemr: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=gmm.scoreb STRIDEthe frequency with which the forces due to the bias should be calculated=2

# print useful info to file
The BIASVALUE action with label emr calculates the following quantities:
 Quantity   
 Description  
emr.bias
the instantaneous value of the bias potential
emr._bias
one or multiple instances of this quantity can be referenced elsewhere in the input filePRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=5000