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

Luke Goodsell luke.goodsell at gmail.com
Thu May 12 11:29:43 CEST 2011

Thanks for your response, Chris.

> 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.

Partly; the only method I knew of was inelegant and likely to cause
bizarre outcomes.

>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.

I am using an implicit solvent, and the macromolecule I wish to hold
rigid accounts for >99% of the atoms in my system. Additional
extensions I later wish to employ are available only for gromacs, so
charmm is not an option for me.

> 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.

Great; I will look into this.

> Chris.


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