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 |
|---|---|---|---|
| -0.8033 -0.5290 0.6226 | -0.8033 -0.5290 0.6226 | 0.1000 0.1000 0.1000 | 0.0002 0.0002 0.0004 |
| 0.7510 -0.2002 -0.4919 | 0.7510 -0.2002 -0.4919 | 0.1000 0.1000 0.1000 | 0.0003 0.0003 0.0004 |
| -1.0116 0.9967 0.9860 | -1.0116 0.9967 0.9860 | 0.1000 0.1000 0.1000 | 0.0004 0.0001 0.0002 |
| -0.7555 -0.7734 -0.7414 | -0.7555 -0.7734 -0.7414 | 0.1000 0.1000 0.1000 | 0.0001 0.0003 0.0002 |
| -0.7263 -0.9806 -0.5037 | -0.7263 -0.9806 -0.5037 | 0.1000 0.1000 0.1000 | 0.0004 0.0002 0.0002 |
| 0.0425 -0.6642 -0.2219 | 0.0425 -0.6642 -0.2219 | 0.1000 0.1000 0.1000 | 0.0004 0.0002 0.0001 |
| -0.5235 1.0074 -0.9848 | -0.5235 1.0074 -0.9848 | 0.1000 0.1000 0.1000 | 0.0001 0.0005 0.0004 |
| -0.1968 -0.7469 -0.7341 | -0.1968 -0.7469 -0.7341 | 0.1000 0.1000 0.1000 | 0.0001 0.0001 0.0004 |
| 0.0088 -0.7528 0.6822 | 0.0088 -0.7528 0.6822 | 0.1000 0.1000 0.1000 | 0.0003 0.0001 0.0004 |
| 0.0076 -0.2703 -0.2816 | 0.0076 -0.2703 -0.2816 | 0.1000 0.1000 0.1000 | 0.0000 0.0003 0.0003 |
| 0.0206 0.9889 -0.9390 | 0.0206 0.9889 -0.9390 | 0.1000 0.1000 0.1000 | 0.0001 0.0002 0.0005 |
| 0.2967 -0.6868 -0.7619 | 0.2967 -0.6868 -0.7619 | 0.1000 0.1000 0.1000 | 0.0003 0.0002 0.0000 |
| 0.7150 -0.4035 0.4290 | 0.7150 -0.4035 0.4290 | 0.1000 0.1000 0.1000 | 0.0002 0.0003 0.0000 |
| 0.7774 -0.7085 -0.5544 | 0.7774 -0.7085 -0.5544 | 0.1000 0.1000 0.1000 | 0.0002 0.0004 0.0004 |
| 0.4690 0.9921 1.0023 | 0.4690 0.9921 1.0023 | 0.1000 0.1000 0.1000 | 0.0003 0.0001 0.0001 |
| 0.7345 -0.7948 -0.8309 | 0.7345 -0.7948 -0.8309 | 0.1000 0.1000 0.1000 | 0.0002 0.0002 0.0003 |
| 0.9562 -0.7797 0.4659 | 0.9562 -0.7797 0.4659 | 0.1000 0.1000 0.1000 | 0.0002 0.0002 0.0005 |
| -0.9618 -0.1272 -0.2316 | -0.9618 -0.1272 -0.2316 | 0.1000 0.1000 0.1000 | 0.0003 0.0000 0.0004 |
| 0.9880 -0.4652 -0.9631 | 0.9880 -0.4652 -0.9631 | 0.1000 0.1000 0.1000 | 0.0003 0.0004 0.0004 |
| -0.7527 -0.2828 -0.7245 | -0.7527 -0.2828 -0.7245 | 0.1000 0.1000 0.1000 | 0.0004 0.0004 0.0005 |
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.