PLUMED-NEST

Project ID: plumID:25.006
Source: Input_Files/Minimum_conformation_extraction/plumed-dumpframes.dat
Originally used with PLUMED version: 2.8.2
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=../MZ1_NPT_300K.part0001.only-protein.pdb

The MOLINFO action with label  calculates somethingph_brd4: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=63-69
The CENTER action with label ph_brd4 calculates the following quantities:
 Quantity   
 Description  
ph_brd4.value
the position of the center of massph_vhl: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that appear in the definition of this center=7-12

The CENTER action with label ph_vhl calculates the following quantities:
 Quantity   
 Description  
ph_vhl.value
the position of the center of massd_ph_brd4_ph_vhl: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ph_brd4,ph_vhl

The DISTANCE action with label d_ph_brd4_ph_vhl calculates the following quantities:
 Quantity   
 Description  
d_ph_brd4_ph_vhl.value
the DISTANCE between this pair of atomsrgyr: GYRATIONCalculate the radius of gyration, or other properties related to it. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69


The GYRATION action with label rgyr calculates the following quantities:
 Quantity   
 Description  
rgyr.value
the radius that was computed from the weightsUPDATE_IFConditional update of other actions. More details ARGthe labels of values that should be used to make the decision on whether to update or not=d_ph_brd4_ph_vhl MORE_THANlower bound=0.5 LESS_THANupper bound=0.6  
UPDATE_IFConditional update of other actions. More details ARGthe labels of values that should be used to make the decision on whether to update or not=rgyr  MORE_THANlower bound=0.54 LESS_THANupper bound=0.565 
WHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-129
DUMPATOMSDump selected atoms on a file. More details ATOMSthe atom indices whose positions you would like to print out=1-129        FILEfile on which to output coordinates; extension is automatically detected=frames.xyz  UNITS the units in which to print out the coordinates=A
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d_ph_brd4_ph_vhl,rgyr FILEthe name of the file on which to output these quantities=colvar_frames.data
UPDATE_IFConditional update of other actions. More details ARGthe labels of values that should be used to make the decision on whether to update or not=d_ph_brd4_ph_vhl        END end 
UPDATE_IFConditional update of other actions. More details ARGthe labels of values that should be used to make the decision on whether to update or not=rgyr                    END end

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d_ph_brd4_ph_vhl,rgyr FILEthe name of the file on which to output these quantities=colvar_all.data