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Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
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Simlist without simid #971

Closed shozebhaider closed 4 years ago

shozebhaider commented 4 years ago

Hi,

I have a set of 200 xtc trajectories that I need to process using HTMD. Since I have not used ACEMD, I do not have a simid associated with it. So when I try to create a simlist using fsims = simlist(glob('./DATA/'), './protein.pdb'), they are all clubbed into simid =0. Is there a way I can associate a simid to them and get it processed without putting them in individual directories?

Many thanks.

stefdoerr commented 4 years ago

Each trajectory needs to be in a separate folder and then you should do glob("./DATA/*/"). This should work

shozebhaider commented 4 years ago

having them in a directory is essential ?

stefdoerr commented 4 years ago

Yes, it's built into HTMD to assume that each independent trajectory is in a different folder. If you don't want to move the files just make directories with symlinks in them.

shozebhaider commented 4 years ago

Got it. Perfect.. many thanks Stefan.