RESET_CELL

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.

Examples

Reset cell to be triangular after a rototranslational fit

Click on the labels of the actions for more information on what each action computes

DUMPATOMS 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=dump-original.xyz 
ATOMS
the atom indices whose positions you would like to print out. 
=1-20 The DUMPATOMS action with label 
FIT_TO_TEMPLATE 
STRIDE
compulsory keyword ( default=1 )
the frequency with which molecules are reassembled. 
=1 
REFERENCE
compulsory keyword 
a file in pdb format containing the reference structure and the atoms involved in
the CV. 
=ref.pdb 
TYPE
compulsory keyword ( default=SIMPLE )
the manner in which RMSD alignment is performed. 
=OPTIMAL The FIT_TO_TEMPLATE action with label 
DUMPATOMS 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=dump-fit.xyz 
ATOMS
the atom indices whose positions you would like to print out. 
=1-20 The DUMPATOMS action with label 
RESET_CELL 
TYPE
compulsory keyword ( default=TRIANGULAR )
the manner in which the cell is reset 
=TRIANGULAR The RESET_CELL action with label 
DUMPATOMS 
FILE
compulsory keyword 
file on which to output coordinates; extension is automatically detected 
=dump-reset.xyz 
ATOMS
the atom indices whose positions you would like to print out. 
=1-20 The DUMPATOMS action with label 

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

Glossary of keywords and components

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