PLUMED-NEST

Project ID: plumID:22.000
Source: plumed-2.2.dat
Originally used with PLUMED version: 2.5
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

INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed-common-2.dat
# The command:
# INCLUDE FILE=plumed-common-2.dat
# ensures PLUMED loads the contents of the file called plumed-common-2.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label plumed-common-2.dat calculates somethingUNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=nm TIMEthe units of time=ps  ENERGYthe units of energy=kj/mol
The UNITS action with label  calculates somethingMOLINFOThis 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=2.pdb
RANDOM_EXCHANGESSet random pattern for exchanges. More details

ab48: COORDINATIONCalculate coordination numbers. More details  GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5452,5453,5454,5455  R_0The r_0 parameter of the switching function=0.45
The COORDINATION action with label ab48 calculates the following quantities:
 Quantity   
 Description  
ab48.value
the value of the coordinationab49: COORDINATIONCalculate coordination numbers. More details  GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5471,5472,5473,5474  R_0The r_0 parameter of the switching function=0.45
The COORDINATION action with label ab49 calculates the following quantities:
 Quantity   
 Description  
ab49.value
the value of the coordinationab50: COORDINATIONCalculate coordination numbers. More details  GROUPAFirst list of atoms=3045,3048,3049,3050,3826,3829,3830,3831  GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=5487,5488,5489,5490  R_0The r_0 parameter of the switching function=0.45

The COORDINATION action with label ab50 calculates the following quantities:
 Quantity   
 Description  
ab50.value
the value of the coordinationanti1: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=377,378,379,380,381,382,383,384,32,33,34,35,36,37,38 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1  STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=inter
The ANTIBETARMSD action with label anti1 calculates the following quantities:
 Quantity   
 Description  
anti1.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti1.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
anti1.value
if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheetanti2: ANTIBETARMSDProbe the antiparallel beta sheet content of your protein structure. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=430,431,432,433,434,435,32,33,34,35,36,37 TYPE the manner in which RMSD alignment is performed=OPTIMAL R_0The r_0 parameter of the switching function=0.1  STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 STYLE Antiparallel beta sheets can either form in a single chain or from a pair of chains=inter

The ANTIBETARMSD action with label anti2 calculates the following quantities:
 Quantity   
 Description  
anti2.struct
the vectors containing the rmsd distances between the residues and each of the reference structures
anti2.lessthan
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold
anti2.value
if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheetcat_site: 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=3043,3824
The CENTER action with label cat_site calculates the following quantities:
 Quantity   
 Description  
cat_site.value
the position of the center of massab48_site: 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=5442,5456
The CENTER action with label ab48_site calculates the following quantities:
 Quantity   
 Description  
ab48_site.value
the position of the center of massab49_site: 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=5456,5475
The CENTER action with label ab49_site calculates the following quantities:
 Quantity   
 Description  
ab49_site.value
the position of the center of massab50_site: 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=5475,5491
The CENTER action with label ab50_site calculates the following quantities:
 Quantity   
 Description  
ab50_site.value
the position of the center of massdis_ab48: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=cat_site,ab48_site
The DISTANCE action with label dis_ab48 calculates the following quantities:
 Quantity   
 Description  
dis_ab48.value
the DISTANCE between this pair of atomsdis_ab49: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=cat_site,ab49_site
The DISTANCE action with label dis_ab49 calculates the following quantities:
 Quantity   
 Description  
dis_ab49.value
the DISTANCE between this pair of atomsdis_ab50: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=cat_site,ab50_site
# --- End of included input --- 
The DISTANCE action with label dis_ab50 calculates the following quantities:
 Quantity   
 Description  
dis_ab50.value
the DISTANCE between this pair of atomsbe2: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=dis_ab48 SIGMAthe widths of the Gaussian hills=0.1 HEIGHTthe heights of the Gaussian hills=0.5 BIASFACTORuse well tempered metadynamics and use this bias factor=4 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 PACEthe frequency for hill addition=2000 FILE a file in which the list of added hills is stored=HILLS GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.05 GRID_MINthe lower bounds for the grid=0 GRID_MAXthe upper bounds for the grid=3.8

The METAD action with label be2 calculates the following quantities:
 Quantity   
 Description  
be2.bias
the instantaneous value of the bias potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=ab48,ab49,dis_ab48,dis_ab49,anti1,anti2 STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=COLVAR
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=dis_ab48,be2.bias STRIDE the frequency with which the quantities of interest should be output=2000 FILEthe name of the file on which to output these quantities=BIAS