[gmx-users] Shrink simulation box while maintaining ensemble

Matthias Ernst matthias.ernst at physik.uni-freiburg.de
Mon Feb 15 16:35:44 CET 2016


I am running a protein folding simulation, starting with an extended
structure that needs a lot of water molecules to fulfill the minimial
image convenction.
Is there a way to "shrink" a simulation box and get rid of unnecessary
solvent molecules while keeping velocities (to preserve the ensemble as
far as possible and avoid re-equilibration)?


Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611

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