Action: RESET_CELL

Module	generic
Description	Usage
This action is used to rotate the full cell

Further details and examples

This action is used to rotate the full cell

Rotating the full cell is useful if you want 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 using 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. You can read the documentation for FIT_TO_TEMPLATE for more detail.

Currently, only TYPE=TRIANGULAR is implemented, which allows one to reset the cell to a lower triangular one. This command finds a proper rotation rotates 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.

[!CAUTION] The implementation of this action is available but should be considered in testing phase. Please report any strange behavior.

[!CAUTION] 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

#SETTINGS INPUTFILES=regtest/basic/rt63/align.pdb
DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump-original.xyz ATOMSthe atom indices whose positions you would like to print out=1-20
The DUMPATOMS action with label  calculates somethingFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details STRIDE the frequency with which molecules are reassembled=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=
regtest/basic/rt63/align.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt63/align.pdb
    
ATOM      1 HH31 ACE     1      -0.000  -0.000  00.000  1.00  0.00            
ATOM      2 HH31 ACE     1      -0.000  -0.000  00.000  0.50  0.00            
END
  
 TYPE the manner in which RMSD alignment is performed=OPTIMAL
DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump-fit.xyz ATOMSthe atom indices whose positions you would like to print out=1-20
RESET_CELLThis action is used to rotate the full cell More details TYPE the manner in which the cell is reset=TRIANGULAR
DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump-reset.xyz ATOMSthe atom indices whose positions you would like to print out=1-20

Syntax

The following table describes the keywords and options that can be used with this action