AW: how to edit restart.coor

From: Norman Geist (
Date: Thu Apr 05 2012 - 01:18:58 CDT



I would follow Aron's suggestion. If you are unlucky while moving atoms by
hand you possibly move atoms into each other, what causes a crashing
simulation. Minimization will also not work then. You could also use the
IMD plugin for that and move the atom away in vmd while the simulation is
already running.


Best wishes


Norman Geist.


Von: [] Im Auftrag
von Aron Broom
Gesendet: Donnerstag, 5. April 2012 00:48
An: Jiao, Dian NMN (-EXP)
Betreff: Re: namd-l: how to edit restart.coor


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


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



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



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

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