This is part of the function module |
Calculates the average over multiple arguments.
If more than one collective variable is given for each argument then they are averaged separately. The average is stored in a component labelled label.cvlabel.
NUM | the number of local replicas |
NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
ARG | the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3... |
The following input tells plumed to calculate the chemical shifts for four different proteins in the same simulation box then average them, calculated the sum of the squared deviation with respect to the experimental values and applies a linear restraint.
MOLINFO STRUCTURE=data/template.pdb chaina: GROUP ATOMS=1-1640 chainb: GROUP ATOMS=1641-3280 chainc: GROUP ATOMS=3281-4920 chaind: GROUP ATOMS=4921-6560 WHOLEMOLECULES ENTITY0=chaina ENTITY1=chainb ENTITY2=chainc ENTITY3=chaind csa: CS2BACKBONE ATOMS=chaina NRES=100 DATA=data/ TEMPLATE=chaina.pdb NOPBC csb: CS2BACKBONE ATOMS=chainb NRES=100 DATA=data/ TEMPLATE=chainb.pdb NOPBC csc: CS2BACKBONE ATOMS=chainc NRES=100 DATA=data/ TEMPLATE=chainc.pdb NOPBC csd: CS2BACKBONE ATOMS=chaind NRES=100 DATA=data/ TEMPLATE=chaind.pdb NOPBC ensca: LOCALENSEMBLE NUM=4 ARG1=(csa\.ca_.*) ARG2=(csb\.ca_.*) ARG3=(csc\.ca_.*) ARG4=(csd\.ca_.*) enscb: LOCALENSEMBLE NUM=4 ARG1=(csa\.cb_.*) ARG2=(csb\.cb_.*) ARG3=(csc\.cb_.*) ARG4=(csd\.cb_.*) ensco: LOCALENSEMBLE NUM=4 ARG1=(csa\.co_.*) ARG2=(csb\.co_.*) ARG3=(csc\.co_.*) ARG4=(csd\.co_.*) enshn: LOCALENSEMBLE NUM=4 ARG1=(csa\.hn_.*) ARG2=(csb\.hn_.*) ARG3=(csc\.hn_.*) ARG4=(csd\.hn_.*) ensnh: LOCALENSEMBLE NUM=4 ARG1=(csa\.nh_.*) ARG2=(csb\.nh_.*) ARG3=(csc\.nh_.*) ARG4=(csd\.nh_.*) stca: STATS ARG=(ensca\.csa\.ca_.*) PARARG=(csa\.expca_.*) SQDEVSUM stcb: STATS ARG=(enscb\.csa\.cb_.*) PARARG=(csa\.expcb_.*) SQDEVSUM stco: STATS ARG=(ensco\.csa\.co_.*) PARARG=(csa\.expco_.*) SQDEVSUM sthn: STATS ARG=(enshn\.csa\.hn_.*) PARARG=(csa\.exphn_.*) SQDEVSUM stnh: STATS ARG=(ensnh\.csa\.nh_.*) PARARG=(csa\.expnh_.*) SQDEVSUM res: RESTRAINT ARG=stca.*,stcb.*,stco.*,sthn.*,stnh.* AT=0.,0.,0.,0.,0. KAPPA=0.,0.,0.,0.,0 SLOPE=16.,16.,12.,24.,0.5