PLUMED-NEST

Project ID: plumID:25.027
Source: metad/input/plumed_input_maxent_onebead.dat
Originally used with PLUMED version: 2.9
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

#SETTINGS NATOMS=269937
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=aacg_template_onebead_SOL.pdb #pdb contains both full atom and martini pdb

The MOLINFO action with label  calculates somethingn: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-5829
The GROUP action with label n calculates somethingh: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=@hydrogensall hydrogen atoms. Click here for more information. 
The GROUP action with label h calculates somethingnnh: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=n REMOVEremove these atoms from the list=h

#WHOLEMOLECULES ENTITY0=nnh
The GROUP action with label nnh calculates somethingWHOLEMOLECULESThis 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=n

## BEADS DEFINITION
#INCLUDE FILE=plumed_beads.dat

#INCLUDE FILE=saxs_qvals_onebead_bias_uf51_stride1.dat

#MOVINGRESTRAINT ...
#   ARG=d 
#   STEP0=0 AT0=1.0 KAPPA0=100.0 
#   STEP1=1000 AT1=2.0 
#   STEP2=2000 AT2=1.0 
#   STEP3=2500 KAPPA3=0.0 
#...

d1: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5558,859
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=5637,859
The DISTANCE action with label d2 calculates the following quantities:
 Quantity   
 Description  
d2.value
the DISTANCE between this pair of atomsd3: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5637,967
The DISTANCE action with label d3 calculates the following quantities:
 Quantity   
 Description  
d3.value
the DISTANCE between this pair of atomsd4: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=5637,1051 

The DISTANCE action with label d4 calculates the following quantities:
 Quantity   
 Description  
d4.value
the DISTANCE between this pair of atomsRg: GYRATIONCalculate the radius of gyration, or other properties related to it. More details TYPE The type of calculation relative to the Gyration Tensor you want to perform=RADIUS ATOMSthe group of atoms that you are calculating the Gyration Tensor for=nnh

The GYRATION action with label Rg calculates the following quantities:
 Quantity   
 Description  
Rg.value
the radius that was computed from the weightsuwall: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=d1,d2,d3,d4 ATthe positions of the wall=3.0,3.0,3.0,3.0 KAPPAthe force constant for the wall=1000.0,1000.0,1000.0,1000.0 EXP the powers for the walls=2,2,2,2 EPS the values for s_i in the expression for a wall=1,1,1,1 OFFSET the offset for the start of the wall=0,0,0,0 


# metadynamics
The UPPER_WALLS action with label uwall calculates the following quantities:
 Quantity   
 Description  
uwall.bias
the instantaneous value of the bias potential
uwall.force2
the instantaneous value of the squared force due to this bias potentialmeta: METADUsed to performed metadynamics on one or more collective variables. More details ...
      ARGthe labels of the scalars on which the bias will act=Rg 
      SIGMAthe widths of the Gaussian hills=0.005 
      HEIGHTthe heights of the Gaussian hills=2.09 # 0.5 kcal/mol
      BIASFACTORuse well tempered metadynamics and use this bias factor=10 
      PACEthe frequency for hill addition=500 
...
#      GRID_MIN=0 
#      GRID_MAX=8 
#      STRIDE=2

The METAD action with label meta calculates the following quantities:
 Quantity   
 Description  
meta.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=* STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=colvar_metad_restr