PLUMED-NEST-TEST-SITE

Project ID: plumID:21.043
Source: PLUMED-NEST/plumed-1.dat
Originally used with PLUMED version: 2.4
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

#RESTART

FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=step5_charmm2gmx-modified.pdb
The FIT_TO_TEMPLATE action with label  calculates somethinga0The FIXEDATOM action with label a0 calculates the following quantities:
 Quantity   
 Type   
 Description  
a0
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0,0,0
a0: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,0  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
azThe FIXEDATOM action with label az calculates the following quantities:
 Quantity   
 Type   
 Description  
az
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=0,0,1
az: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=0,0,1  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0
phiThe TORSION action with label phi calculates the following quantities:
 Quantity   
 Type   
 Description  
phi
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=70,143,a0,az
thetaThe TORSION action with label theta calculates the following quantities:
 Quantity   
 Type   
 Description  
theta
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details ATOMSthe four atoms involved in the torsional angle=2549,2420,a0,az

##ZANGLES ATOMS=70,143 LABEL=phi
##ZANGLES ATOMS=2549,2420 LABEL=theta
# Activate metadynamics in phi and psi
# depositing a Gaussian every 500 time steps,
# with height equal to 1.0 kJoule/mol,
# and width 0.35 rad for both CVs. 

METADUsed to performed metadynamics on one or more collective variables. More details ...
LABELa label for the action so that its output can be referenced in the input to other actions=metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential
ARGthe labels of the scalars on which the bias will act=phi,theta
PACEthe frequency for hill addition=500
HEIGHTthe heights of the Gaussian hills=1.0
SIGMAthe widths of the Gaussian hills=0.35,0.35
FILE a file in which the list of added hills is stored=HILLS
BIASFACTORuse well tempered metadynamics and use this bias factor=10.0
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310.0
GRID_MINthe lower bounds for the grid=-pi,-pi
GRID_MAXthe upper bounds for the grid=pi,pi
GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.1,0.1
... METAD

PRINTPrint quantities to a file. More details STRIDE the frequency with which the quantities of interest should be output=500 ARGthe labels of the values that you would like to print to the file=phi,theta,metad.bias FILEthe name of the file on which to output these quantities=COLVAR