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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed May 11 18:44:07 CEST 2011

If I read between the lines correctly, you know how to do this in  
gromacs, but you wish that you got a big speedup from freezing most of  
the atoms in your system. If that is the case, then I think that  
gromacs can not help you in its current form. Therefore, I suggest  
that you try the Charmm software. It may be slower overall, but it  
gives you the speedup you expect when you freeze 95% of the atoms in  
your system so it may be much faster for your usage. Other software  
may also do this, but I have no experience with it. If you have  
explicit water, this won't be of much use since you're still only  
freezing <10% of the atoms in your system.

If you simply want to know how to freeze one structure, then use  
freeze groups and energy exclusions without pressure coupling, or use  
position restraints and refcoordscaling=com with position restraints,  
or create an elastic network of restraints.


-- original message --


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,

More information about the gromacs.org_gmx-users mailing list