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 |
|---|---|---|---|
| 4.4000 5.8527 3.6786 | 4.4000 5.8527 3.6786 | 0.0050 0.0050 0.0050 | 0.0572 0.0381 0.0000 |
| 4.5104 5.8235 3.5867 | 4.5104 5.8235 3.5867 | 0.0050 0.0050 0.0050 | 0.0954 0.0191 0.0572 |
| 4.3815 5.9549 3.7440 | 4.3815 5.9549 3.7440 | 0.0050 0.0050 0.0050 | 0.0286 0.0477 0.1001 |
| 4.5717 5.7348 3.6134 | 4.5717 5.7348 3.6134 | 0.0050 0.0050 0.0050 | 0.0858 0.0572 0.0811 |
| 4.5723 5.9137 3.5670 | 4.5723 5.9137 3.5670 | 0.0050 0.0050 0.0050 | 0.0191 0.0572 0.0620 |
| 4.4666 5.8095 3.4855 | 4.4666 5.8095 3.4855 | 0.0050 0.0050 0.0050 | 0.0763 0.0286 0.0381 |
| 4.3282 5.7474 3.6919 | 4.3282 5.7474 3.6920 | 0.0050 0.0050 0.0050 | 0.0668 0.0572 0.0620 |
| 4.2072 5.7455 3.7624 | 4.2072 5.7455 3.7624 | 0.0050 0.0050 0.0050 | 0.0572 0.0858 0.0381 |
| 4.2200 5.7578 3.9122 | 4.2200 5.7578 3.9122 | 0.0050 0.0050 0.0050 | 0.1049 0.0191 0.0572 |
| 4.1886 5.8623 3.9704 | 4.1886 5.8623 3.9704 | 0.0050 0.0050 0.0050 | 0.0286 0.0095 0.0381 |
| 4.1251 5.6153 3.7418 | 4.1251 5.6153 3.7418 | 0.0050 0.0050 0.0050 | 0.0381 0.0763 0.0238 |
| 4.0885 5.5946 3.5975 | 4.0885 5.5946 3.5975 | 0.0050 0.0050 0.0050 | 0.0191 0.0381 0.0048 |
| 4.1483 5.4964 3.5112 | 4.1483 5.4964 3.5112 | 0.0050 0.0050 0.0050 | 0.0954 0.0477 0.0572 |
| 3.9740 5.6610 3.5464 | 3.9740 5.6610 3.5464 | 0.0050 0.0050 0.0050 | 0.0572 0.0858 0.0572 |
| 4.1021 5.4757 3.3808 | 4.1021 5.4757 3.3808 | 0.0050 0.0050 0.0050 | 0.0191 0.0954 0.0858 |
| 3.9262 5.6392 3.4120 | 3.9262 5.6392 3.4120 | 0.0050 0.0050 0.0050 | 0.0000 0.0858 0.0763 |
| 3.9923 5.5461 3.3271 | 3.9923 5.5461 3.3271 | 0.0050 0.0050 0.0050 | 0.0000 0.0381 0.1001 |
| 3.9482 5.5229 3.1919 | 3.9482 5.5229 3.1919 | 0.0050 0.0050 0.0050 | 0.0763 0.0095 0.1001 |
| 4.3606 5.6617 3.6527 | 4.3606 5.6617 3.6527 | 0.0050 0.0050 0.0050 | 0.0572 0.0572 0.0811 |
| 4.1496 5.8312 3.7305 | 4.1496 5.8311 3.7305 | 0.0050 0.0050 0.0050 | 0.0191 0.1049 0.0572 |
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.