PLUMED-NEST

Project ID: plumID:20.026
Source: plumed.dat
Originally used with PLUMED version: 2.5
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

rmsd_a: MULTI_RMSDCalculate RMSD distances for different domains and combine them. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=OBP_lis_final.pdb TYPE the manner in which RMSD alignment is performed=MULTI-OPTIMAL
The MULTI_RMSD action with label rmsd_a calculates the following quantities:
 Quantity   
 Description  
rmsd_a.value
the sum of the multiple RMSD distancesrmsd_b: MULTI_RMSDCalculate RMSD distances for different domains and combine them. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=OBP_lsd_final.pdb TYPE the manner in which RMSD alignment is performed=MULTI-OPTIMAL
The MULTI_RMSD action with label rmsd_b calculates the following quantities:
 Quantity   
 Description  
rmsd_b.value
the sum of the multiple RMSD distancesRESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=rmsd_a,rmsd_b  ATthe position of the restraint=0.375,0.425   KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100000.0,100000.0 LABELa label for the action so that its output can be referenced in the input to other actions=restraint
The RESTRAINT action with label restraint calculates the following quantities:
 Quantity   
 Description  
restraint.bias
the instantaneous value of the bias potential
restraint.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=rmsd_a,rmsd_b,restraint.bias STRIDE the frequency with which the quantities of interest should be output=100 FILEthe name of the file on which to output these quantities=COLVAR