PLUMED-NEST

Project ID: plumID:26.001
Source: input_files/Wobble-Prot/5-Equil/chain-B/rep1/equil_B_P_1.dat
Originally used with PLUMED version: 2.8
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

d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3030,566
The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Description  
d1.value
the DISTANCE between this pair of atomsd2: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=3027,563
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsermsd: eRMSDCalculate eRMSD with respect to a reference structure. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=/leonardo_scratch/large/userexternal/tfernand/Projects/Alx-ribo/A-Prot/ermsd_ref.pdb ATOMSthe list of atoms (use lcs)=3032,3026,3035,3066,3060,3069,533,529,525,565,559,555
The ERMSD action with label ermsd calculates the following quantities:
 Quantity   
 Description  
ermsd.value
the eRMSD between the instantaneous structure and the reference structure that was inputrestr: ...
    RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details 
    ARGthe values the harmonic restraint acts upon=ermsd 
    ATthe position of the restraint=0.2 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=10000
    ...
The RESTRAINT action with label restr calculates the following quantities:
 Quantity   
 Description  
restr.bias
the instantaneous value of the bias potential
restr.force2
the instantaneous value of the squared force due to this bias potentialPRINTPrint 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=equil_B_P_1.out STRIDE the frequency with which the quantities of interest should be output=1000