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m3g / packmol

Packmol - Initial configurations for molecular dynamics simulations
http://m3g.github.io/packmol
MIT License
214 stars 48 forks source link

Packing, Saving intermediate PDB files #40

Closed stippner closed 1 year ago

stippner commented 1 year ago

Hello,

thank you very much for providing such a nice and intuitive tool. Right now I want to pack multiple molecules strands into one big cube. For that I am interested in dumping intermediate files during the packing process in order to understand better how the actual packing is performed. Is there any way to do that?

Best regards, Simon

lmiq commented 1 year ago

You can use this option:

Write the current point to output file even if it is worse than the the best point so far (used for checking purposes only): Usage: writebad

to write all structures obtained, after each optimization loop.

Another feature that might be useful is this one:

http://leandro.iqm.unicamp.br/m3g/packmol/userguide.shtml#restart