Positions are passed correctly

PLUMED must receive the positions from an MD code in order to calculate CVs correctly.
To test these positions are passed correctly to PLUMED we run a short trajectory and output the positions of all the atoms that are passed to PLUMED using the following command:

Click on the labels of the actions for more information on what each action computes
tested on2.9
tested onmaster
DUMPATOMS
Dump selected atoms on a file. More details
 
ATOMS
the atom indices whose positions you would like to print out
=
@mdatoms
refers to all the MD codes atoms but not PLUMEDs vatoms. Click here for more information. 
 
FILE
file on which to output coordinates; extension is automatically detected
=plumed.xyz

Trajectory

Input and output files for the test calculation are available in this zip archive

Results

Calculations were not sucessful and no data was generated for comparison

The table below includes some of the results from the calculation. The columns contain:

  1. The positions that were obtained from the MD code, $x_{md}$.
  2. The positions that were obtained from PLUMED, $x_{pl}$.
  3. The tolerances that were used when comparing these quantities, $\delta$.
  4. The values of $100\frac{\vert x_{md} - x_{pl}\vert }{ \delta }$.

If the PLUMED interface is working correctly the first two sets of numbers should be identical and the final column should be filled with zeros.