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

From: Jiao, Dian NMN (-EXP) (
Date: Wed Apr 04 2012 - 17:56:38 CDT

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).


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

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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