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 |
|---|---|---|---|
| 0.1310 0.5550 1.6220 | 0.1310 0.5550 1.6220 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0000 |
| 0.0980 0.5970 1.7010 | 0.0980 0.5970 1.7010 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0000 |
| 0.0930 0.6050 1.5500 | 0.0930 0.6050 1.5500 | 0.0010 0.0010 0.0010 | 0.0007 0.0060 0.0000 |
| 0.1234 0.5648 1.6227 | 0.1234 0.5648 1.6227 | 0.0010 0.0010 0.0010 | 0.4001 0.3994 0.2980 |
| 1.6130 0.9900 0.9920 | 1.6130 0.9900 0.9920 | 0.0010 0.0010 0.0010 | 0.0119 0.0060 0.0000 |
| 1.5990 0.9830 1.0860 | 1.5990 0.9830 1.0860 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0000 |
| 1.7000 1.0290 0.9830 | 1.7000 1.0290 0.9830 | 0.0010 0.0010 0.0010 | 0.0119 0.0119 0.0000 |
| 1.6208 0.9934 1.0011 | 1.6208 0.9934 1.0011 | 0.0010 0.0010 0.0010 | 0.2027 0.3994 0.2027 |
| 0.3770 0.7530 1.3170 | 0.3770 0.7530 1.3170 | 0.0010 0.0010 0.0010 | 0.0000 0.0060 0.0119 |
| 0.3350 0.7870 1.3960 | 0.3350 0.7870 1.3960 | 0.0010 0.0010 0.0010 | 0.0030 0.0000 0.0119 |
| 0.4440 0.6920 1.3490 | 0.4440 0.6920 1.3490 | 0.0010 0.0010 0.0010 | 0.0030 0.0000 0.0000 |
| 0.3797 0.7501 1.3288 | 0.3797 0.7501 1.3288 | 0.0010 0.0010 0.0010 | 0.2980 0.0000 0.0954 |
| 0.6670 2.0350 1.4470 | 0.6670 2.0350 1.4470 | 0.0010 0.0010 0.0010 | 0.0000 0.0238 0.0119 |
| 0.6570 1.9410 1.4320 | 0.6570 1.9410 1.4320 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0119 |
| 0.6110 2.0520 1.5230 | 0.6110 2.0520 1.5230 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0000 |
| 0.6600 2.0268 1.4535 | 0.6600 2.0268 1.4535 | 0.0010 0.0010 0.0010 | 0.0954 0.3815 0.2980 |
| 1.8230 1.7170 1.0270 | 1.8230 1.7170 1.0270 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0000 |
| 1.8670 1.7540 1.1040 | 1.8670 1.7540 1.1040 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0000 |
| 1.7370 1.7590 1.0270 | 1.7370 1.7590 1.0270 | 0.0010 0.0010 0.0010 | 0.0000 0.0000 0.0000 |
| 1.8185 1.7254 1.0352 | 1.8185 1.7254 1.0352 | 0.0010 0.0010 0.0010 | 0.0954 0.2980 0.3934 |
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.