Re: Symmetry in NAMD, how to achieve during a MD simulation?

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Oct 27 2010 - 18:37:35 CDT

Just because a structure has an inherent symmetry does not mean the dynamics will also be symmetric. That being said, we are currently implementing in NAMD ways to impose symmetry-based restraints to force the structure to maintain a given symmetry over time.

On Oct 27, 2010, at 10:46 AM, Wendy González wrote:

> Dear NAMD users:
>
> I am running MD simulations of symmetrical structures: potassium channels. And I do not see the same interactions between the atoms in one monomer regarding to the other during the MD simulations. Maybe the time of my dynamics is not enough to see a symmetrical development? Could you give me more information about this point? About the limit of MD simulation to see these symmetrical states?

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