PLUMED-NEST

Project ID: plumID:26.001
Source: input_files/Wobble-Prot/4-Steered/chain-A/rep2/steered_A_P_2.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 inputmr: ...
    MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details 
    ARGthe labels of the scalars on which the bias will act=ermsd 
    AT0ATx is equal to the position of the restraint at time STEPx=1.442655 STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=10000
    AT1ATx is equal to the position of the restraint at time STEPx=0.0 STEP1This keyword appears multiple times as STEPx with x=0,1,2,=100000000 KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=10000
    ...
The MOVINGRESTRAINT action with label mr calculates the following quantities:
 Quantity   
 Description  
mr.bias
the instantaneous value of the bias potential
mr.work
the total work performed changing this restraint
mr.force2
the instantaneous value of the squared force due to this bias potential
mr._cntr
one or multiple instances of this quantity can be referenced elsewhere in the input file
mr._work
one or multiple instances of this quantity can be referenced elsewhere in the input file
mr._kappa
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=steered_A_P_2.out STRIDE the frequency with which the quantities of interest should be output=1000