VMD-L Mailing List

From: Anna Modzelewska (amodzelewska_at_iimcb.gov.pl)
Date: Wed Jun 22 2005 - 11:51:22 CDT

Yes, it works!!!!!!

Thanks a lot!
Anna
  ----- Original Message -----
  From: Jordi Cohen
  To: Anna Modzelewska
  Cc: vmd_at_ks.uiuc.edu
  Sent: Wednesday, June 22, 2005 6:39 PM
  Subject: Re: vmd-l: autoimd on windows

  A follow-up.

  I had a second look at the autoimd.tcl source, and it appears as though
  the copying of the parameter file to the scratch directory may have been
  prevented on Windows. I am attaching a version of AutoIMD that will fix
  this specific problem (i.e. your param files will now be copied to your
  scratch directory before running NAMD).

  To make this work, startup VMD normally. Then, before starting autoimd, do
  a "source autoimd.tcl" on the attached file (or alternatively, "File->Load
  State..." on this file should work too).

  Then run AutoIMD as before and hopefully it should just work. Let me know
  if this fixes the problem.

  Cheers,
  jordi

  On Wed, 22 Jun 2005, Anna Modzelewska wrote:

> John,
> I think I found the source of my problem, but I don't know how to fix it.
> I upgraded namd to v2.5 and I still got the same error. When I run namd manually it works correctly. I tried to do the test that you recomended, and I received an error: "unable to open parameter file, abnormal program termination". In the imd.nadm file I typed in the exact path to the parameter and structure files. After that namd run correctly and I could connect to the simulation with vmd. I did the same thing with Autoimd. I submited the job from the autoimd window, then changed the autoimd.namd file (I inputed the paths for parameters and structure), then run namd manually and finally connected the simulation from the autoimd window. It worked.
> Is there a way to make the autoimd plugin insert the exact path to required simulation files in the *.namd files?
>
> Anna
>
>
> ----- Original Message -----
> From: John Stone
> To: Anna Modzelewska
> Cc: vmd-l_at_ks.uiuc.edu ; namd-l_at_ks.uiuc.edu
> Sent: Tuesday, June 21, 2005 10:43 PM
> Subject: Re: vmd-l: autoimd on windows
>
>
>
> Anna,
> It's possible that you've found a bug in either AutoIMD itself, or
> in the Windows version of NAMD. Can you try running NAMD manually on
> your Windows machine and see if it starts up and runs a simple simulation ok?
> Do you get a similar "abnormal program termination" message if you run
> NAMD by itself, or only when run from the AutoIMD plugin?
> There's a simple IMD test system you can load and run manually if you
> aren't already familiar with NAMD.
> http://www.ks.uiuc.edu/Training/Tutorials/science/10Ala-tutorial/10Ala-html/index.html
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jun 20, 2005 at 01:40:29PM +0200, Anna Modzelewska wrote:
> > Hi,
> > I'm fighting with AutoIMD. I tried to run a simulation on PC with WindowsXP and anotherone with Windows2000. On both I got the same error: "Attempt to connnect to the simulation timed out!" and the information in the log file: "abnormal program termination" (see attached file). It can not be a fault of my input files (I took the tutorial files from the nanotube tutorial). Maybe I should precise some additional paths in plugin's files?
> >
> > Does anyone use AutoIMD on Windows PC? Did it work without any problems?
> > Please, help!!!
> >
> > Anna
> >
> >
> > ************************************************************************
> > Anna Modzelewska, M.Sc. amodzelewska_at_iimcb.gov.pl
> > International Institute of Molecular and Cell Biology
> > http://www.iimcb.gov.pl/
> > Trojdena 4, 02-109 Warsaw, Poland
> > phone: +48 22 5970721 fax: +48 22 5970715
> > ************************************************************************
> >
>
>
>
> --
> 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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