From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Thu Apr 09 2020 - 23:05:41 CDT
One quick answer - a comment on the same line as a command needs to use ;#.
With regards to the lack of output, I don’t know what CHARMMGUI NAMD input files look like. I highly recommend looking to the NAMD tutorial for an example and then figure out what is missing from your input.
Best,
JC
> On Apr 9, 2020, at 10:32 PM, Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca> wrote:
>
> Hello,
>
> Simple question: I used CHARMMGUI NAMD input equilibration files and used NAMD2 to get output and log files, yet I don't get .coor .vel and .xsc of equilibration step 6.1 so step 6.2 gives me fatal error that its unable to open extended file system.
>
> I reduced numsteps and run steps but the issue persists. It now also says
>
> Reason: FATAL ERROR: too many args
> while executing
> "run 50000 #50 ps"
> (file "step6.1_equilibration.inp" line 171)
>
> Charm++ fatal error:
> FATAL ERROR: too many args
> while executing
> "run 50000 #50 ps"
> (file "step6.1_equilibration.inp" line 171)
>
> Abort (core dumped)
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Unable to open extended system file.
>
>
>
> Please help me out, been stuck for days and I haven't received a reply earlier.
>
> Thank you.
>
> Best,
>
> Asma
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