From: Jordi Cohen (
Date: Wed Jun 15 2005 - 13:13:25 CDT


It is not clear what the problem is. Is it possible for you to send
me a copy of the PDB/PSF files that you are using as well as the
AutoIMD parameters (e.g., selection, special param files), so that I
can test your system over here and see if I can reproduce the error?

It appears (though this needs to be verified), that your NAMD job
died by itself before VMD/AutoIMD could connect to it. If you run
namd2 directly using the "E:/autoimd/autoimd.namd" config file
created by AutoIMD, do you know if NAMD runs normally, or if it
aborts in a similar way? This will help us determine if the problem
is with AutoIMD or with NAMD (AutoIMD simply creates and runs the
autoimd.namd job, and then connects to it; if running that job aborts
unexpectedly, then AutoIMD will not be able to start...).


On Jun 15, 2005, at 9:35 AM, Anna Modzelewska wrote:

> Hi,
> I try to do a simulation with AutoIMD with VMD1.8.3 and NAMD 2.5b1
> on Windows PC. After a few seconds a get an error: "Attempt to
> connnect to the simulation timed out!"
> In attached .log file I found only the information about "abnormal
> program termination".
> In the VMDTkConsole was written:
> Info: writing psf file E:/autoimd/autoimd.psf
> total of 66 atoms
> total of 65 bonds
> total of 96 angles
> total of 31 dihedrals
> total of 32 impropers
> Info: psf file complete.
> submitJob returned local localhost 1680
> Error killing simulation.
> couldn't execute "kill": no such file or directory
> Done with AutoIMD.
> Anyone has an idea what is wrong?
> Regards
> Anna
> **********************************************************************
> **
> Anna Modzelewska, M.Sc.
> International Institute of Molecular and Cell Biology
> Trojdena 4, 02-109 Warsaw, Poland
> phone: +48 22 5970721 fax: +48 22 5970715
> **********************************************************************
> **