[gmx-users] Rigid structure and flexible structure present in sing system

Luke Goodsell luke.goodsell at gmail.com
Wed May 11 18:16:39 CEST 2011


For a while I've been looking for a way to include a rigid
(macromolecular) structure and a flexible (small-protein) structure in
a single system and have not had much success.

I looked for a way to apply a different set of constraints to each
structure, but couldn't find one. I looked into modifying the topology
file, but the only method I could find was to artificially increase
the mass of every atom in the rigid structure and this does not save
any computing time.

Does anyone know how I can fix the relative co-ordinates of one
structure and only calculate the MD of another?

Any constructive criticism (even if to inform me that I'm doing
something ridiculous) is very gratefully received.

Kind regards,

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