PLUMED-NEST

Project ID: plumID:26.001
Source: input_files/Wobble-Prot/4-Steered/chain-C/rep2/plumed_test_metad_params.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

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=/leonardo_scratch/large/userexternal/tfernand/Projects/Alx-ribo/A-Deprot/chain-C/01_box-min/ref.pdb
The MOLINFO action with label  calculates somethingrA: 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-Deprot/chain-C/01_box-min/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 rA calculates the following quantities:
 Quantity   
 Description  
rA.value
the eRMSD between the instantaneous structure and the reference structure that was inputrB: 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=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 rB calculates the following quantities:
 Quantity   
 Description  
rB.value
the eRMSD between the instantaneous structure and the reference structure that was inputS_var: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=rA,rB FUNCthe function you wish to evaluate=(x^2-y^2)/(2*1.109468) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label S_var calculates the following quantities:
 Quantity   
 Description  
S_var.value
an arbitrary functionZ_var: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARGthe values input to this function=rA,rB,S_var FUNCthe function you wish to evaluate=((x^2+y^2)/(2)-(z^2)-((1.109468^2)/4))^0.5 PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
The MATHEVAL action with label Z_var calculates the following quantities:
 Quantity   
 Description  
Z_var.value
an arbitrary functionPRINTPrint 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=metad_test_C_rep2 STRIDE the frequency with which the quantities of interest should be output=1