PLUMED-NEST

Project ID: plumID:19.007
Source: EMMI-MT/plumed.dat
Originally used with PLUMED version: 2.6-dev
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

# include topology info: this is needed to identify atom types
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 WHOLE The reference structure is whole, i
# define all heavy atoms using GROMACS index file
# which can be created with gmx_mpi make_ndx
The MOLINFO action with label  calculates somethingprotein-hThe GROUP action with label protein-h calculates the following quantities:
 Quantity   
 Type   
 Description  
protein-h
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 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
proteinThe GROUP action with label protein calculates the following quantities:
 Quantity   
 Type   
 Description  
protein
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 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
protein-no-negativeThe GROUP action with label protein-no-negative calculates the following quantities:
 Quantity   
 Type   
 Description  
protein-no-negative
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 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-no-negative-no-h
# make protein whole: add reference position of first heavy atom (in nm)
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ADDREFERENCE Define the reference position of the first atom of each entity using a PDB file EMST only for backward compatibility, as of PLUMED 2 ENTITY0the atoms that make up a molecule that you wish to align=protein
# create EMMI score
EMMICalculate 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=gmmThe EMMI action with label gmm calculates the following quantities:
 Quantity   
 Type   
 Description  
gmm.scoreb
scalar
Bayesian score
gmm.neff
scalar
effective number of replicas NOPBC ignore the periodic boundary conditions when calculating distances TEMPtemperature=300.0 NL_STRIDEThe frequency with which we are updating the neighbor list=50 NL_CUTOFFThe cutoff in overlap for the neighbor list=0.01
ATOMSatoms for which we calculate the density map, typically all heavy atoms=protein-no-negative GMM_FILEfile with the parameters of the GMM components=AC_SYMM.dat
#ATOMS selects what is refined
# no-negative-no-h or no-h are reasonable
# resolution is not used - no Bfactor fitting
# SIGMA_MIN can go down to 0.02, must be > NL_CUTOFF,
# if crashes, raise back to 0.05,
# the larger the number the softer the contribution of the EM data
SIGMA_MINminimum uncertainty=0.05 RESOLUTIONCryo-EM map resolution=0.1 NOISETYPEfunctional form of the noise (GAUSS, OUTLIERS, MARGINAL)=MARGINAL
...

# translate into bias
emrThe BIASVALUE action with label emr calculates the following quantities:
 Quantity   
 Type   
 Description  
emr.bias
scalar
the instantaneous value of the bias potential
emr.gmm.scoreb_bias
scalar
one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named gmm.scoreb: 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
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=gmm.* 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