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
 |
 |
DUMPATOMSDump selected atoms on a file. More detailsATOMS=the atom indices whose positions you would like to print out@mdatomsrefers to all the MD codes atoms but not PLUMEDs vatoms. Click here for more information.FILE=plumed.xyzfile on which to output coordinates; extension is automatically detected
Trajectory
Input and output files for the test calculation are available inthis zip archive
Results
| MD code output | PLUMED output | Tolerance | % Difference |
|---|---|---|---|
| -0.0663 -0.0663 -0.0663 | -0.0663 -0.0663 -0.0663 | 0.0010 0.0010 0.0010 | 0.0398 0.0398 0.0398 |
| 0.0663 0.0663 0.0663 | 0.0663 0.0663 0.0663 | 0.0010 0.0010 0.0010 | 0.0398 0.0398 0.0398 |
| -0.0663 -0.0663 -0.0663 | -0.0663 -0.0663 -0.0663 | 0.0010 0.0010 0.0010 | 0.0471 0.0408 0.0115 |
| 0.0663 0.0663 0.0663 | 0.0663 0.0663 0.0663 | 0.0010 0.0010 0.0010 | 0.0471 0.0408 0.0115 |
| -0.0663 -0.0663 -0.0663 | -0.0663 -0.0663 -0.0663 | 0.0010 0.0010 0.0010 | 0.0220 0.0192 0.0063 |
| 0.0663 0.0663 0.0663 | 0.0663 0.0663 0.0663 | 0.0010 0.0010 0.0010 | 0.0220 0.0192 0.0063 |
| -0.0664 -0.0664 -0.0664 | -0.0664 -0.0664 -0.0664 | 0.0010 0.0010 0.0010 | 0.0309 0.0023 0.0032 |
| 0.0664 0.0664 0.0664 | 0.0664 0.0664 0.0664 | 0.0010 0.0010 0.0010 | 0.0309 0.0023 0.0032 |
| -0.0665 -0.0664 -0.0665 | -0.0665 -0.0664 -0.0665 | 0.0010 0.0010 0.0010 | 0.0060 0.0137 0.0184 |
| 0.0665 0.0664 0.0665 | 0.0665 0.0664 0.0665 | 0.0010 0.0010 0.0010 | 0.0060 0.0137 0.0184 |
| -0.0666 -0.0665 -0.0666 | -0.0666 -0.0665 -0.0666 | 0.0010 0.0010 0.0010 | 0.0180 0.0096 0.0084 |
| 0.0666 0.0665 0.0666 | 0.0666 0.0665 0.0666 | 0.0010 0.0010 0.0010 | 0.0180 0.0096 0.0084 |
| -0.0667 -0.0667 -0.0667 | -0.0667 -0.0667 -0.0667 | 0.0010 0.0010 0.0010 | 0.0269 0.0210 0.0448 |
| 0.0667 0.0667 0.0667 | 0.0667 0.0667 0.0667 | 0.0010 0.0010 0.0010 | 0.0269 0.0210 0.0448 |
| -0.0669 -0.0668 -0.0669 | -0.0669 -0.0668 -0.0669 | 0.0010 0.0010 0.0010 | 0.0205 0.0005 0.0224 |
| 0.0669 0.0668 0.0669 | 0.0669 0.0668 0.0669 | 0.0010 0.0010 0.0010 | 0.0205 0.0005 0.0224 |
| -0.0670 -0.0669 -0.0670 | -0.0670 -0.0669 -0.0670 | 0.0010 0.0010 0.0010 | 0.0217 0.0494 0.0316 |
| 0.0670 0.0669 0.0670 | 0.0670 0.0669 0.0670 | 0.0010 0.0010 0.0010 | 0.0217 0.0494 0.0316 |
| -0.0672 -0.0671 -0.0672 | -0.0672 -0.0671 -0.0672 | 0.0010 0.0010 0.0010 | 0.0349 0.0126 0.0184 |
| 0.0672 0.0671 0.0672 | 0.0672 0.0671 0.0672 | 0.0010 0.0010 0.0010 | 0.0349 0.0126 0.0184 |
The table below includes some of the results from the calculation. The columns contain:
- The positions that were obtained from the MD code, $x_{md}$.
- The positions that were obtained from PLUMED, $x_{pl}$.
- The tolerances that were used when comparing these quantities, $\delta$.
- 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.