Re: how to edit restart.coor

From: Aron Broom (
Date: Wed Apr 04 2012 - 17:47:52 CDT

I think that usually the .coor files are written in PDB-like format no?
They should be easy to edit/understand just by opening them up in vim,
gedit, nano or something of that sort. You'll likely introduce some atomic
clashes by doing this, but as you say I suspect you can minimize for a
short period and then another short equilibration. Alternatively, you can
take your equilibrated system, and just apply a harmonic potential to steer
the ion to where you want it, that shouldn't take a lot of time and the
rest of your system will remain at equilibrium (unless you use some kind of
extreme force).


On Wed, Apr 4, 2012 at 6:29 PM, Jiao, Dian NMN (-EXP) <>wrote:

> Hi,
> Is there a way to edit the restart.coor file? It should be the file that
> has the coordinates of all the atoms, right? I wanted to modify the
> position of a sodium after the system has been equilibrated and start a new
> run. In stead of placing the ion at a new position and equilibrate it from
> the very beginning, it'd be easier to just make small changes to the
> restart coordinates. Maybe it still needs to be equilibrated at least
> locally around the sodium's new location, it would save a lot of time.
> Thanks
> Dian

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

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