Dual Topology Generator for Alchemical Pathways

pmx
1

I have a few questions regarding the online generator for Dual topologies for free energy calculations.

  1. Does this generator also include the use of a water model (tip3p)? If not, how would I account for this? I ask this because the tutorial on http://pmx.mpibpc.mpg.de/sardinia2018_tutorial1/index.html states that I can do the first three steps using the generator at this link http://pmx.mpibpc.mpg.de/contact.html, and one of the three steps mentioned involves assigning the water model for simulations. So, would I have to include the water model of interest manually before/after using the generator, or does the generator account for this already?

  2. The pmx tutorial ( the first link mentioned) is for comparing folding stabilities, but can it also be used to analyze the stability of loop closure? If so, what modifications would I need to do to this tutorial for such purpose?

2

This is a very old post, but maybe it can still be relevant:

  1. hybrid topology generation does not require water model definition. It does not matter whether the water definition is added to the .top file before or after hybrid topology construction.

  2. loop closure would require creating/breaking a covalent bond. This is not supported by the standard alchemical calculations.

Vytas