VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Thu Apr 09 2020 - 22:04:49 CDT

Keep vmd-l on the line. .coor and .vel files are written only at the end of
the simulation. So step 6.1 didn't finish. Take a look at the log for that
step.
Josh

On Thu, Apr 9, 2020, 8:55 PM Khoualdi Asma Feriel <
asma.feriel.khoualdi_at_umontreal.ca> wrote:

> Dear Mr Vermaas,
>
> Thank you so much for your kind and prompt reply. Is there also a
> potential problem I may not have been aware of that causes .coor .vel
> and .xsc files of equilibration step 6.1 to not be produced ?
>
> Thank you.
>
> Sincerely,
>
> Asma
> ------------------------------
> *From:* Josh Vermaas <joshua.vermaas_at_gmail.com>
> *Sent:* April 9, 2020 10:46 PM
> *To:* NAMD list <namd-l_at_ks.uiuc.edu>; Khoualdi Asma Feriel <
> asma.feriel.khoualdi_at_umontreal.ca>
> *Subject:* Re: namd-l: .coor and .vel output files not generated
>
> You need a semicolon between the run command and the comment. That is the
> line that NAMD is complaining about.
> Josh
>
> On Thu, Apr 9, 2020, 8:41 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
>
>