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 details ATOMSthe 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. FILEfile on which to output coordinates; extension is automatically detected=plumed.xyz
Trajectory
Input and output files for the test calculation are available inthis zip archive
Results
| MD code output | PLUMED output | Tolerance | % Difference |
|---|---|---|---|
| 0.2140 0.2847 0.2704 | 0.2140 0.2847 0.2704 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0000 |
| -0.0365 0.3711 0.4730 | -0.0365 0.3711 0.4730 | 0.0010 0.0010 0.0010 | 0.0302 0.0000 0.0000 |
| -0.1738 0.1497 -0.1158 | -0.1738 0.1497 -0.1158 | 0.0010 0.0010 0.0010 | 0.0000 0.0015 0.0000 |
| -0.1217 -0.1865 0.0202 | -0.1217 -0.1865 0.0202 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0101 |
| -0.2651 -0.4901 0.5564 | -0.2651 -0.4901 0.5564 | 0.0010 0.0010 0.0010 | 0.0030 0.0030 0.0000 |
| -0.4733 -0.4491 0.8607 | -0.4733 -0.4491 0.8607 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0000 |
| 0.2531 0.3479 -0.0373 | 0.2531 0.3479 -0.0373 | 0.0010 0.0010 0.0010 | 0.0030 0.0000 0.0101 |
| 0.8986 0.0902 0.7634 | 0.8986 0.0902 0.7634 | 0.0010 0.0010 0.0010 | 0.0060 0.0097 0.0000 |
| -0.3242 -0.0259 0.6101 | -0.3242 -0.0259 0.6101 | 0.0010 0.0010 0.0010 | 0.0030 0.0300 0.0000 |
| -0.4032 0.1957 1.4358 | -0.4032 0.1957 1.4358 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.1907 |
| -0.0570 0.3496 1.8918 | -0.0570 0.3496 1.8918 | 0.0010 0.0010 0.0010 | 0.0101 0.0000 0.1073 |
| 0.2147 0.6595 1.6085 | 0.2147 0.6595 1.6085 | 0.0010 0.0010 0.0010 | 0.0000 0.0060 0.3099 |
| -0.3639 0.0943 0.2945 | -0.3639 0.0943 0.2945 | 0.0010 0.0010 0.0010 | 0.0000 0.0402 0.0000 |
| 0.5568 0.8450 0.1085 | 0.5568 0.8450 0.1085 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0000 |
| 0.7377 1.3563 0.6784 | 0.7377 1.3563 0.6784 | 0.0010 0.0010 0.0010 | 0.0060 0.1073 0.0000 |
| 0.7683 0.7698 0.6266 | 0.7683 0.7698 0.6266 | 0.0010 0.0010 0.0010 | 0.0000 0.0060 0.0060 |
| 0.7533 0.4442 1.2598 | 0.7533 0.4442 1.2598 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.5007 |
| -0.1769 0.8971 1.2285 | -0.1769 0.8971 1.2286 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.3099 |
| 0.3582 1.3107 0.9772 | 0.3582 1.3107 0.9772 | 0.0010 0.0010 0.0010 | 0.0000 0.2980 0.0060 |
| 0.5294 0.1529 0.3884 | 0.5294 0.1529 0.3884 | 0.0010 0.0010 0.0010 | 0.0000 0.0015 0.0000 |
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.