VMD-L Mailing List

From: Claw Isthelaw (clawisthelaw_at_hotmail.com)
Date: Sun May 20 2007 - 16:20:30 CDT

Hi John,

Thanks for the suggestion. I have a shell script that executes an NAMD simulation of a protein in water and simultaneously fires up VMD, just for visual inspection and interest. Automatically shutting down VMD after the simulation completes is just for keeping a clean workspace, nothing more. How would I go about monitoring the incoming IMD timesteps. I have some tcl experience, but just have a difficult time getting started.

Jeff

----------------------------------------
> Date: Sun, 20 May 2007 13:13:04 -0500
> From: johns_at_ks.uiuc.edu
> To: clawisthelaw_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Automatically shutting down VMD after NAMD terminates IMD connection
>
>
> Hi,
> I don't think there's a straightforward way to do this at the moment,
> but one way you could do it is to keep track of the last time VMD received
> an incoming IMD timestep, and if no new timesteps occured for a predetermined
> amount of time, fire off a Tcl callback to shutdown VMD etc.
> I could probably create new callbacks expressly for the purpose of
> tracking the status of IMD connections in a future rev of VMD if this
> would be helpful to you.
>
> What are you doing with the VMD that's listening to NAMD via IMD?
> Is this just intended as an ease-of-use improvement or are you using
> VMD as an additional simulation logging mechanism of some sort?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Sat, May 19, 2007 at 06:23:42PM +0000, Claw Isthelaw wrote:
> >
> > Dear VMD Community,
> >
> > Does anyone know a way I can command VMD (running interactively with NAMD) to shut down after NAMD finishes its simulation? This would be placed within a script so that I do not have to do it myself.
> >
> > Jeff Tibbitt
> > _________________________________________________________________
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>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078

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