PLUMED-NEST

Project ID: plumID:25.027
Source: steered_input/onebead/plumed_input_steered_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

INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=saxs_qvals_onebead_bias_uf51.dat
# The command:
# INCLUDE FILE=saxs_qvals_onebead_bias_uf51.dat
# ensures PLUMED loads the contents of the file called saxs_qvals_onebead_bias_uf51.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label saxs_qvals_onebead_bias_uf51.dat calculates somethingSAXSCalculates SAXS intensity. More details ... #action name also at the end
LABELa label for the action so that its output can be referenced in the input to other actions=saxs #just a label
ATOMSThe atoms to be included in the calculation, e=1-5829 #atom group generated with script in plumed_beads.dat
ONEBEAD calculate SAXS for a single bead model
TEMPLATE A PDB file is required for ONEBEAD mapping=aacg_template_onebead.pdb
#GPU
SOLVDENS Density of the solvent to be used for the correction of atomistic form factors=0.334
SOLVATION_CORRECTION Solvation layer electron density correction (ONEBEAD only)=0.080
SOLVATION_STRIDE Number of steps between every new residues solvation estimation via LCPO (ONEBEAD only)=100 # 100 in production, 1 in driver
SASA_CUTOFF SASA value to consider a residue as exposed to the solvent (ONEBEAD only)=0.7

NOPBC Ignore the periodic boundary conditions when calculating distances

SCALE_EXPINT Scaling value for experimental data normalization=0.033474980320492204
QVALUE1Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.0101178 EXPINT1Add an experimental value for each q value=0.03268278549019608
QVALUE2Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.02004692 EXPINT2Add an experimental value for each q value=0.029574363529411757
QVALUE3Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.02997605 EXPINT3Add an experimental value for each q value=0.02573280137254901
QVALUE4Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.03990518 EXPINT4Add an experimental value for each q value=0.021441139215686255
QVALUE5Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.04996495 EXPINT5Add an experimental value for each q value=0.017315874509803902
QVALUE6Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.06002473 EXPINT6Add an experimental value for each q value=0.013607859411764688
QVALUE7Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.06995385 EXPINT7Add an experimental value for each q value=0.010560911352941158
QVALUE8Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.08001363 EXPINT8Add an experimental value for each q value=0.007967748960784298
QVALUE9Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.08994276 EXPINT9Add an experimental value for each q value=0.006012438235294102
QVALUE10Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1000025 EXPINT10Add an experimental value for each q value=0.004477551431372533
QVALUE11Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1199914 EXPINT11Add an experimental value for each q value=0.00240160503921567
QVALUE12Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1399803 EXPINT12Add an experimental value for each q value=0.0011963419411764554
QVALUE13Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1599692 EXPINT13Add an experimental value for each q value=0.0006005266058823376
QVALUE14Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.1799581 EXPINT14Add an experimental value for each q value=0.0003499681941176316
QVALUE15Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.199947 EXPINT15Add an experimental value for each q value=0.00024375893686272957
QVALUE16Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2200666 EXPINT16Add an experimental value for each q value=0.00023157075156861204
QVALUE17Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2400555 EXPINT17Add an experimental value for each q value=0.0002318339798039062
QVALUE18Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2600444 EXPINT18Add an experimental value for each q value=0.00018894343299998486
QVALUE19Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, =0.2800333 EXPINT19Add an experimental value for each q value=0.00017391225274508286
#QVALUE20=0.3000000 EXPINT20=0.00011380315192155344 # rounded q val, should be fine..
#QVALUE20=0.3000222 EXPINT20=0.00011380315192155344
... SAXS
# --- End of included input --- 
#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 
#...

The SAXS action with label saxs calculates the following quantities:
 Quantity   
 Description  
saxs.score
the Metainference score
saxs.sigma
uncertainty parameter
saxs.sigmaMean
uncertainty in the mean estimate
saxs.neff
effective number of replicas
saxs.acceptSigma
MC acceptance for sigma values
saxs.q
The # SAXS of qsteered: MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
   ARGthe labels of the scalars on which the bias will act=saxs.q-0,saxs.q-1,saxs.q-2,saxs.q-3,saxs.q-4,saxs.q-5,saxs.q-6,saxs.q-7,saxs.q-8,saxs.q-9,saxs.q-10,saxs.q-11,saxs.q-12,saxs.q-13,saxs.q-14,saxs.q-15,saxs.q-16,saxs.q-17,saxs.q-18
   STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0 
   AT0ATx is equal to the position of the restraint at time STEPx=0.979278,0.921347,0.833486,0.725885,0.607986,0.491325,0.384933,0.290743,0.213274,0.150629,0.068293,0.028521,0.014037,0.010561,0.009581,0.008204,0.006521,0.005074,0.004155
   KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0
   STEP1This keyword appears multiple times as STEPx with x=0,1,2,=2500000
   AT1ATx is equal to the position of the restraint at time STEPx=0.97633472,0.88347665,0.76871745,0.64051238,0.51727811,0.40650836,0.31548671,0.23802102,0.17960991,0.13375815,0.07174328,0.03573839,0.01793957,0.01045462,0.00728182,0.00691773,0.00692559,0.00564432,0.00519529
   KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0,1000000.0
...

# PRINT
#PRINT ARG=(saxs\.q-.*) STRIDE=500 FILE=colvar_saxs_martini
The MOVINGRESTRAINT action with label steered calculates the following quantities:
 Quantity   
 Description  
steered.bias
the instantaneous value of the bias potential
steered.work
the total work performed changing this restraint
steered.force2
the instantaneous value of the squared force due to this bias potential
steered._cntr
one or multiple instances of this quantity can be referenced elsewhere in the input file
steered._work
one or multiple instances of this quantity can be referenced elsewhere in the input file
steered._kappa
one or multiple instances of this quantity can be referenced elsewhere in the input filePRINTPrint 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_steered_106_10ns_onebead