UWALLS
 This is part of the manyrestraints module It is only available if you configure PLUMED with ./configure –enable-modules=manyrestraints . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

Add UPPER_WALLS restraints on all the multicolvar values

This action takes the set of values calculated by the colvar specified by label in the DATA keyword and places a restraint on each quantity, $$x$$, with the following functional form:

$$k((x-a+o)/s)^e$$

$$k$$ (KAPPA) is an energy constant in internal unit of the code, $$s$$ (EPS) a rescaling factor and $$e$$ (EXP) the exponent determining the power law. By default: EXP = 2, EPS = 1.0, OFF = 0.

Examples

The following set of commands can be used to stop a cluster composed of 20 atoms subliming. The position of the center of mass of the cluster is calculated by the COM command labelled c1. The DISTANCES command labelled d1 is then used to calculate the distance between each of the 20 atoms in the cluster and the center of mass of the cluster. These distances are then passed to the UWALLS command, which adds a UPPER_WALLS restraint on each of them and thereby prevents each of them from moving very far from the center of mass of the cluster.

Click on the labels of the actions for more information on what each action computes
c1: COM ATOMSthe list of atoms which are involved the virtual atom's definition. =1-20
d1: DISTANCES GROUPACalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB.
=c1 GROUPBCalculate the distances between all the atoms in GROUPA and all the atoms in GROUPB.
=1-20
sr: UWALLS DATAcompulsory keyword
certain actions in plumed work by calculating a list of variables and summing over
them. =d1 ATcompulsory keyword
the radius of the sphere =2.5 KAPPAcompulsory keyword
the force constant for the wall. =0.2

Glossary of keywords and components
Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

 Quantity Description bias the instantaneous value of the bias potentials

In addition the following quantities can be calculated by employing the keywords listed below

 Quantity Keyword Description gradient GRADIENT the gradient vmean VMEAN the norm of the mean vector. The output component can be referred to elsewhere in the input file by using the label.vmean vsum VSUM the norm of sum of vectors. The output component can be referred to elsewhere in the input file by using the label.vsum spath SPATH the position on the path gspath GPATH the position on the path calculated using trigonometry gzpath GPATH the distance from the path calculated using trigonometry zpath ZPATH the distance from the path altmin ALT_MIN the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous. between BETWEEN the number/fraction of values within a certain range. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters. highest HIGHEST the highest of the quantities calculated by this action lessthan LESS_THAN the number of values less than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters. lowest LOWEST the lowest of the quantities calculated by this action max MAX the maximum value. This is calculated using the formula described in the description of the keyword so as to make it continuous. mean MEAN the mean value. The output component can be referred to elsewhere in the input file by using the label.mean min MIN the minimum value. This is calculated using the formula described in the description of the keyword so as to make it continuous. moment MOMENTS the central moments of the distribution of values. The second moment would be referenced elsewhere in the input file using label.moment-2, the third as label.moment-3, etc. morethan MORE_THAN the number of values more than a target value. This is calculated using one of the formula described in the description of the keyword so as to make it continuous. You can calculate this quantity multiple times using different parameters. sum SUM the sum of values
Compulsory keywords
 DATA certain actions in plumed work by calculating a list of variables and summing over them. This particular action can be used to calculate functions of these base variables or prints them to a file. This keyword thus takes the label of one of those such variables as input. AT the radius of the sphere KAPPA the force constant for the wall. The k_i in the expression for a wall. OFFSET ( default=0.0 ) the offset for the start of the wall. The o_i in the expression for a wall. EXP ( default=2.0 ) the powers for the walls. The e_i in the expression for a wall. EPS ( default=1.0 ) the values for s_i in the expression for a wall
Options
 NUMERICAL_DERIVATIVES ( default=off ) calculate the derivatives for these quantities numerically SERIAL ( default=off ) do the calculation in serial. Do not use MPI LOWMEM ( default=off ) lower the memory requirements TIMINGS ( default=off ) output information on the timings of the various parts of the calculation