Re: How to fix relative position of a group

From: JC Gumbart (
Date: Tue Oct 13 2009 - 19:27:40 CDT

You should first ask yourself why they should be fixed. Do they
leave the binding sites during simulation? Perhaps there is a reason
for that if they do. The force field usually can model bound ions,
although not always perfectly.

If you still want to artificially constrain them, there are a few
ways to do so, using either extraBonds or collective variable-based
restraints in NAMD 2.7, or even manually adding the bonds to the psf
(and correspondingly to your parameter file).

On Oct 13, 2009, at 3:40 PM, Yang wrote:

> Hi all,
> I am running NAMD simulations on a peptide system containing two
> copper binding sites in both ends of the peptide. During the MD run,
> I wanted to keep the RELATIVE position of each copper binding group
> but let the whole group move together during the simulation. Is
> there any way to do this using NAMD? Thank you very much!!!
> Zhongyu Yang

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