This is part of the generic module

This action is used to rotate the full cell

This can be used to modify the periodic box. Notice that this is done at fixed scaled coordinates, so that also atomic coordinates for the entire system are affected. To see what effect try the DUMPATOMS directive to output the atomic positions.

Also notice that PLUMED propagate forces correctly so that you can add a bias on a CV computed after rotation. See also FIT_TO_TEMPLATE

Currently, only TYPE=TRIANGULAR is implemented, which allows one to reset the cell to a lower triangular one. Namely, a proper rotation is found that allows rotating the box so that the first lattice vector is in the form (ax,0,0), the second lattice vector is in the form (bx,by,0), and the third lattice vector is arbitrary.

Attention: The implementation of this action is available but should be considered in testing phase. Please report any strange behavior.; This directive modifies the stored position at the precise moment it is executed. This means that only collective variables which are below it in the input script will see the corrected positions. Unless you know exactly what you are doing, leave the default stride (1), so that this action is performed at every MD step.

Compulsory keywords

STRIDE	( default=1 ) the frequency with which molecules are reassembled. Unless you are completely certain about what you are doing leave this set equal to 1!
TYPE	( default=TRIANGULAR ) the manner in which the cell is reset

Examples

Reset cell to be triangular after a rototranslational fit

DUMPATOMS FILE=dump-original.xyz ATOMS=1-20
FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=OPTIMAL
DUMPATOMS FILE=dump-fit.xyz ATOMS=1-20
RESET_CELL TYPE=TRIANGULAR
DUMPATOMS FILE=dump-reset.xyz ATOMS=1-20

The reference file for the FIT_TO_TEMPLATE is just a normal pdb file with the format shown below:

ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H
ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C
ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H
ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H
ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O
END