Implementation of time-dependent topology

[KaiSzuttor]

It should be possible to read a time-dependent topology, e.g. for MC, grand canonical or reaction ensemble simulations.

[kain88-de]

This is partially possible with TRR files. The timestep object also reads the lambda value from the file in the current development version. We currently don't do anything with that information though.

[jbarnoud]

Time-dependent topology will also be needed for full support of Gromacs's TNG format.

[richardjgowers]

So are we talking about changing the number of atoms? Or just changing all
possible properties of atoms?

On Mon, 30 May 2016, 17:23 Jonathan Barnoud, notifications@github.com
wrote:

Time-dependent topology will also be needed for full support of Gromacs's
TNG format.

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[jbarnoud]

I do not know for HALMD, but TNG support changing the number of atoms. At least, it is what I understand from:

It is also possible to change the number of molecules from one frame set to another, which is necessary to simulate grand canonical ensembles. In that case, the number of frames per frame set must be set to 1 (if the number of particles can change every frame), which means that multiframe compression cannot be used. Figure 1 provides an overview of the file structure.

[orbeckst]

Re TNG format: We should probably support it in the future – does anyone care to open an issue?