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
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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 |
|---|---|---|---|
| -0.0039 -0.0009 0.0010 | -0.0039 -0.0009 0.0010 | 0.0010 0.0010 0.0010 | 0.0300 0.0300 0.0400 |
| 0.8477 -0.0013 0.8430 | 0.8477 -0.0013 0.8430 | 0.0010 0.0010 0.0010 | 0.0298 0.0300 0.0060 |
| 0.8367 0.8409 0.0046 | 0.8367 0.8409 0.0046 | 0.0010 0.0010 0.0010 | 0.0298 0.0358 0.0400 |
| 0.0060 0.8476 0.8330 | 0.0060 0.8476 0.8330 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0179 |
| 0.0005 0.0053 1.6733 | 0.0005 0.0053 1.6733 | 0.0010 0.0010 0.0010 | 0.0300 0.0200 0.0477 |
| 0.8440 0.0041 2.5159 | 0.8440 0.0041 2.5159 | 0.0010 0.0010 0.0010 | 0.0298 0.0400 0.0238 |
| 0.8413 0.8407 1.6782 | 0.8413 0.8407 1.6782 | 0.0010 0.0010 0.0010 | 0.0298 0.0060 0.0238 |
| -0.0016 0.8379 2.5225 | -0.0016 0.8379 2.5225 | 0.0010 0.0010 0.0010 | 0.0300 0.0298 0.0238 |
| -0.0114 0.0014 3.3583 | -0.0114 0.0014 3.3583 | 0.0010 0.0010 0.0010 | 0.0400 0.0200 0.0238 |
| 0.8322 0.0012 4.2008 | 0.8322 0.0012 4.2008 | 0.0010 0.0010 0.0010 | 0.0119 0.0400 0.0477 |
| 0.8446 0.8438 3.3586 | 0.8446 0.8438 3.3586 | 0.0010 0.0010 0.0010 | 0.0358 0.0000 0.0238 |
| -0.0034 0.8430 4.1987 | -0.0034 0.8430 4.1987 | 0.0010 0.0010 0.0010 | 0.0300 0.0417 0.0477 |
| 0.0058 1.6746 0.0031 | 0.0058 1.6746 0.0031 | 0.0010 0.0010 0.0010 | 0.0000 0.0119 0.0100 |
| 0.8327 1.6827 0.8370 | 0.8327 1.6827 0.8370 | 0.0010 0.0010 0.0010 | 0.0238 0.0238 0.0417 |
| 0.8415 2.5197 -0.0046 | 0.8415 2.5197 -0.0046 | 0.0010 0.0010 0.0010 | 0.0060 0.0000 0.0200 |
| 0.0037 2.5197 0.8356 | 0.0037 2.5197 0.8356 | 0.0010 0.0010 0.0010 | 0.0100 0.0238 0.0298 |
| -0.0035 1.6794 1.6888 | -0.0035 1.6794 1.6888 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0238 |
| 0.8280 1.6711 2.5157 | 0.8280 1.6711 2.5157 | 0.0010 0.0010 0.0010 | 0.0000 0.0119 0.0477 |
| 0.8406 2.5202 1.6915 | 0.8406 2.5202 1.6915 | 0.0010 0.0010 0.0010 | 0.0298 0.0000 0.0238 |
| 0.0097 2.5279 2.5226 | 0.0097 2.5279 2.5226 | 0.0010 0.0010 0.0010 | 0.0400 0.0238 0.0238 |
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.