Validation of buildH

buildH reconstructs hydrogens from a united-atom trajectory and calculates the order parameter on each reconstructed C-H bond. To validate buildH, we took an all-atom POPC trajectory generated with the CHARMM36 force field. First, we removed the hydrogens and reconstructed them with buildH. Then we compared the H reconstruction and the order parameter values calculated with buildH to the real ones from the all-atom trajectory. The output of buildH was also compared to two scripts made by Josef Melcr and Angel Pineiro.

Here is a report made in August 2019 describing this validation.

All the files used for making this validation have been deposited on Zenodo with the following DOI: 10.5281/zenodo.4715962.

Below is shown an animated gif highlighting the tiny difference between the hydrogens in a CHARMM36 POPC vs those reconstructed by buildH.

Note that this validation was made in August 2019. You can retrieve the corresponding old version of buildH here.