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 in this zip archive
Results
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.
| 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 |