Project ID: plumID:25.027
Source: steered_input/martini/plumed_input_steered.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
tested onv2.10
tested onmaster
#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.pdb #pdb contains both full atom and martini pdb

n: 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 h: 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. nnh: 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 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=n # 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
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details. Show included file FILEfile to be included=saxs_qvals_mergedMOB.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 #...
steered: 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=0.982084,0.930479,0.851101,0.752377,0.642163,0.530654,0.42635,0.33136,0.250777,0.183385,0.08982,0.040028,0.018854,0.012057,0.009974,0.008409,0.006692,0.005197,0.004279 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 PRINTPrint 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_m