PMF Accumulator
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PMFLib v6 introduces a new generic format for storing accumulated data from MD simulations. This format is not backward compatible with the previous PMFLib versions. Moreover, the support for the previous formats was completely removed from the PMFLib code. This means that it is not possible to restart simulations performed in PMFLib prior v6.
The PMF accumulator can contain the following major blocks:
| Leading Character | Comment |
|---|---|
| # | trajectory blocks |
| % | header sections |
| @ | data sections |
Trajectory Snapshots
| Key | Comment |
|---|---|
| #ACCUTRAJ | The key is on the first line and it indicates that the file contains a trajectory of PMF accumulators. |
| #ACCUSNAP Num(I10) | The key indicates the beginning of the PMF accumulator snapshot. The number (Num) is not necessary the serial index of the snapshot, but it can indicate, for example, the MD step or number of deposited Gaussian hills in MTD. |
Header Sections
| Key | Content of the next line |
|---|---|
| %PMFLIB-V6 | Number of CVs |
| %VERSION | PMFLib version |
| %METHOD | method abbreviation |
| %DRIVER | driver name |
| %TEMPERATURE | temperature in the internal unit |
| %CVS | multiple lines, specification of CVs |
| %ENERGY-UNIT | conversion factor from the internal unit to the requested unit and the name of the requested unit, see General_setup for unit specification |
| %TEMPERATURE-UNIT | conversion factor from the internal unit to the requested unit and the name of the requested unit, see General_setup for unit specification |