Re: [EXTERNAL] Re: how to edit restart.coor

From: Aron Broom (
Date: Wed Apr 04 2012 - 18:26:43 CDT

Ahh I see. Well, I don't know the official way to convert back, but I see
two options:

1) use that pdb for your restart, using coordinates rather than
bincoordinates (or whatever the keywords are).

2) use the pdb to start a new run of 0 steps and have it output in binary,
and then take that and use it for your binary restart.

Maybe one of those would work.

On Wed, Apr 4, 2012 at 6:56 PM, Jiao, Dian NMN (-EXP) <>wrote:

> My restart.coor file is binary. I can load it in VMD and save as pdb
> without any problems. But how do I convert it back to the binary format
> after editing it, so that I could use it for restart? The SMD method you
> suggested is worth a try though. Thanks
> From: Aron Broom <>
> Date: Wed, 4 Apr 2012 18:47:52 -0400
> To: Dian Jiao <>
> Cc: "" <>
> Subject: [EXTERNAL] 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 force).
> ~Aron
> 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

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

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