 |
 |
 |
| |
|
|
| This is part of the adjmat module | |
| It is only available if you configure PLUMED with ./configure –enable-modules=adjmat . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list. |
Adjacency matrix in which two molecules are adjacent if they are within a certain cutoff and if the angle between them is within certain ranges.
In this case the elements of the adjacency matrix are calculated using:
\[ A_{ij} = \sigma(r_{ij}) \sum_n K_n(\theta_{ij}) \]
In this expression \(r_{ij}\) is the distance between molecule \(i\) and molecule \(j\) and \(\sigma(r_{ij}\) is a switchingfunction that acts on this distance. The $K_n functions are kernelfunctions that take the torsion angle, \(\theta_{ij}\), between the internal orientation vectors for molecules \(i\) and \(j\) as input. These kernel functions should be set so that they are equal to one when the relative orientation of the moleclues are as they are in the solid and equal to zero otherwise. As the above matrix element is a product of functions it is only equal to one when the centers of mass of molecules \(i\) and \(j\) are with a certain distance of each other and when the molecules are aligned in some desirable way.
| ATOMS | The list of molecules for which you would like to calculate the contact matrix. The molecules involved must have an orientation so your list will be a list of the labels of MultiColvar or MultiColvar functions as PLUMED calculates the orientations of molecules within these operations. Please note also that the majority of MultiColvar and MultiColvar functions do not calculate a molecular orientation.. For more information on how to specify lists of atoms see Groups and Virtual Atoms |
| ATOMSA | The list of molecules that you would like to use for the rows of the contact matrix. The molecules involved must have an orientation so your list will be a list of the labels of MultiColvar or MultiColvar functions as PLUMED calculates the orientations of molecules within these operations. Please note also that the majority of MultiColvar and MultiColvar functions do not calculate a molecular orientation. |
| ATOMSB | The list of molecules that you would like to use for the columns of the contact matrix. The molecules involved must have an orientation so your list will be a list of the labels of MultiColvar or MultiColvar functions as PLUMED calculates the orientations of molecules within these operations. Please note also that the majority of MultiColvar and MultiColvar functions do not calculate a molecular orientation. |
| NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |
| NOPBC | ( default=off ) ignore the periodic boundary conditions when calculating distances |
| SERIAL | ( default=off ) do the calculation in serial. Do not parallelize |
| TIMINGS | ( default=off ) output information on the timings of the various parts of the calculation |
| HIGHMEM | ( default=off ) use a more memory intensive version of this collective variable |
| SWITCH | This keyword is used if you want to employ an alternative to the continuous swiching function defined above. The following provides information on the switchingfunction that are available. When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords. You can use multiple instances of this keyword i.e. SWITCH1, SWITCH2, SWITCH3... |
| KERNEL | The various kernels that are used to determine whether or not the molecules are aligned You can use multiple instances of this keyword i.e. KERNEL1, KERNEL2, KERNEL3... |
In the following example an adjacency matrix is constructed in which the \((i,j)\) element is equal to one if molecules \(i\) and \(j\) are within 6 angstroms of each other and if the torsional angle between the orientations of these molecules is close to 0 or \(\pi\). The various connected components of this matrix are determined using the DFSCLUSTERING algorithm and then the size of the largest cluster of connectes molecules is output to a colvar file
UNITS LENGTH=A
MOLECULES ...
MOL1=1,2,1
MOL2=5,6,5
MOL3=9,10,9
MOL4=13,14,13
MOL5=17,18,17
LABEL=m1
... MOLECULES
SMAC_MATRIX ...
ATOMS=m1 SWITCH={RATIONAL D_0=5.99 R_0=0.1 D_MAX=6.0}
KERNEL1={TRIANGULAR CENTER=0 SIGMA=1.0} KERNEL2={TRIANGULAR CENTER=pi SIGMA=0.6}
LABEL=smacm
... SMAC_MATRIX
dfs1: DFSCLUSTERING MATRIX=smacm
cc2: CLUSTER_NATOMS CLUSTERS=dfs1 CLUSTER=1
PRINT ARG=smac.*,cc1.*,cc2 FILE=colvar
1.8.14