MobleyLab / relative-solvation-paper

Paper on reproducibility of relative solvation free energies across packages
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Reviewer 1-Q4: mention other codes #37

Closed Steboss closed 6 years ago

Steboss commented 6 years ago

It is clear that any comparative study has to draw the line somewhere. Nevertheless, it might be useful to briefly describe NAMD's capabilities (though I concede it is a moving target). Further, it is not clear to me whether all recent developments in AMBER have been taken into account (e.g., the already mentioned work by Giese and York (10.1021/acs.jctc.7b01175))

davidlmobley commented 6 years ago

I would deal with this (and similar comments if they occur later) by explicitly discussing in the paper the need to continue this work by running benchmarks on:

halx commented 6 years ago

We clearly say that we use AMBER in version 16, so no newer code. I briefly mention that NAMD is dual--topology and thus "out-of-scope".