Project ID: plumID:19.057
Source: diubq_k63/plumed-main.dat
Originally used with PLUMED version: 2.6
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
tested onv2.10
tested onmaster
#SETTINGS NREPLICAS=2 NATOMS=117366
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=aacgmodel.pdb
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=1-2473

### BEADS DEFINITION
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed-beads.dat 


### METADYNAMICS
#
# CV DEFINITION
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed-cv.dat
# PB-METAD
PBMETADUsed to performed Parallel Bias metadynamics. More details ...
 	#GRID_RFILES=../GRID.cv1,../GRID.cv2,../GRID.hyd,../GRID.pol  
	ARGthe labels of the scalars on which the bias will act=cv1,cv2,hyd,pol
	ADAPTIVEuse a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme=DIFF SIGMAthe widths of the Gaussian hills=2000	
	SIGMA_MINthe lower bounds for the sigmas (in CV units) when using adaptive hills=0.01,0.01,0.01,0.05
	HEIGHTthe height of the Gaussian hills, one for all biases=1.0
	PACEthe frequency for hill addition, one for all biases=200
	BIASFACTORuse well tempered metadynamics with this bias factor, one for all biases=30
	LABELa label for the action so that its output can be referenced in the input to other actions=pb
	GRID_MINthe lower bounds for the grid=-0.6,-1.2,0,0        
        GRID_MAXthe upper bounds for the grid=2.1,1.5,800,800
	WALKERS_MPI Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR
	GRID_WSTRIDEfrequency for dumping the grid=5000000
	GRID_WFILESdump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES=GRID.cv1,GRID.cv2,GRID.hyd,GRID.pol
... PBMETAD


### METAINFERENCE
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed-saxsCG.dat
saxsbias: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=(saxsdata\.score) STRIDEthe frequency with which the forces due to the bias should be calculated=10 

### MONITOR
# SAXS-AA
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=plumed-saxsAA.dat
# ENSEMBLE AND STATISTICS
ens: ENSEMBLECalculates the replica averaging of a collective variable over multiple replicas. More details ARGthe labels of the values from which the function is calculated=(saxsdata\.q-.*),(saxsallatom\.q-.*),pb.bias REWEIGHT simple REWEIGHT using the latest ARG as energy
statsaxs: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=(ens\.saxsdata\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(saxsdata\.exp-.*)
statsaa: STATSCalculates statistical properties of a set of collective variables with respect to a set of reference values. More details ARGthe labels of the values from which the function is calculated=(ens\.saxsallatom\.q-.*) PARARGthe input for this action is the scalar output from one or more other actions without derivatives=(saxsallatom\.exp-.*)

### PRINT
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(saxsdata\.score),(saxsdata\.biasDer),(saxsdata\.weight),(saxsdata\.scale),(saxsdata\.acceptScale),(saxsdata\.acceptSigma),(saxsdata\.sigma.*) STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=BAYES.SAXS
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=statsaxs.*,(ens\.saxsdata\.q-.*) STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=ST.SAXS
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(saxsdata\.q-.*) STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=QVAL
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=statsaa.*,(ens\.saxsallatom\.q-.*) STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=ST.SAXSAA
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=(saxsallatom\.q-.*) STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=QVALAA
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cv1,cv2,hyd,pol,pb.bias STRIDE the frequency with which the quantities of interest should be output=500 FILEthe name of the file on which to output these quantities=CVS

ENDPLUMEDTerminate plumed input. More details