RE: Steering colvars to defined points in space

From: Tristan Croll (
Date: Sun Jan 26 2014 - 22:44:09 CST

Hi Aron,

I'll look into the dummy atoms approach. Distance between the center of mass of my picked atoms and a fixed dummy atom should indeed give me what I want. I've never used them before, but I'm guessing it won't be too difficult.



From: Aron Broom []
Sent: Monday, 27 January 2014 11:24 AM
To: Tristan Croll
Subject: Re: namd-l: Steering colvars to defined points in space

You can't redefine those maps to be relative?
If not, I believe you can use dummy atoms in the colvars, and a dummy atom can be defined to have (x,y,z) coordinates. I've not actually done it, so can't help beyond that, but I think the user guide gives pretty good information.

On Sun, Jan 26, 2014 at 7:10 PM, Tristan Croll <<>> wrote:
Hi all,

I'm currently trying to fit some cryoelectron tomography maps. The resolution is low enough to be very ambiguous, but there are a number of points which can be assigned with relative confidence (e.g. hinge points between domains). I'd like to steer the relevant portions of the structure into these spots, but as far as I can tell the colvars functionality only allows steering into relative rather than absolute coordinates. Is there a simple way to do this?



Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:04 CST