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| 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.
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 quanties 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 refererred to elsewhere in the input file by using the label.vmean |
| vsum | VSUM | the norm of sum of vectors. The output component can be refererred 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 lowest of the quantitities 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 quantitities 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 refererred 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 |
| 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 |
| NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
| SERIAL | ( default=off ) do the calculation in serial. Do not parallelize |
| LOWMEM | ( default=off ) lower the memory requirements |
| TIMINGS | ( default=off ) output information on the timings of the various parts of the calculation |
The following set of commands can be used to stop a cluster composed of 20 atoms subliming. The position of the centre 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 centre of mass of the cluster.
COM ATOMS=1-20 LABEL=c1 DISTANCES GROUPA=c1 GROUPB=1-20 LABEL=d1 UWALLS DATA=d1 AT=2.5 KAPPA=0.2 LABEL=sr
1.8.14