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

From: Victor Ovchinnikov (
Date: Wed Apr 04 2012 - 18:38:09 CDT

vmd > mol load namdbin restart.coor
vmd > animate write namdbin new_restart.coor
On Wed, 2012-04-04 at 22:56 +0000, 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

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:50 CST