Re: .coor and .vel output files not generated

From: Khoualdi Asma Feriel (asma.feriel.khoualdi_at_umontreal.ca)
Date: Fri Apr 10 2020 - 11:12:24 CDT

Thank you all very much.

The semi colon was the problem, the files are now all produced.

Sincerely,

Asma Feriel
________________________________
From: Chandni Tiwari <chandni.tiwari_at_monash.edu>
Sent: April 10, 2020 2:37 AM
To: Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca>
Subject: Re: namd-l: .coor and .vel output files not generated

PS

I again looked at the config file and if its the corrected version which u sent me:

Line 72

# These are specified by CHARMM
exclude scaled1-4; # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4"

U missed the semicolon there. So usually there has to be a semicolon after the command and before the comments "#" if u r doing so on the same line (More details: https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node26.html (ctrl+F "semi colon" to read specifically about semicolon))

On Fri, 10 Apr 2020 at 16:29, Chandni Tiwari <chandni.tiwari_at_monash.edu<mailto:chandni.tiwari_at_monash.edu>> wrote:
Hi Khoualdi,

Looking at the input file and the comments given by others it looks like the "semicolon" between command and # comments might have been the issue, which you have now corrected. So hopefully it should work now. (Your input file looks good to me, still, let me know is it the same file which gave the error or u have sent me the edited one after fixing semicolon thing?)

Also, I am assuming it is just a practice run? If so, I would suggest you try the same output frequency for all, just for now. For, eg:
Instead of this:
restartfreq 1000;
dcdfreq 5000;
xstFreq 5000;
outputEnergies 125;
outputTiming 1000;

Try same frequency for all, like this:
restartfreq 1000;
dcdfreq 1000;
xstFreq 1000;
outputEnergies 1000;
outputTiming 1000;

Not sure if that would help, but just in case if you are still facing the issue, you can try this once.

Let me know if it helps (even if it is not, still let me know so that I can think more on this)

On Fri, 10 Apr 2020 at 15:35, Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca<mailto:asma.feriel.khoualdi_at_umontreal.ca>> wrote:
Dear all,

Thank you so much for your reply. I fixed the semi colon issue in the following

Reason: FATAL ERROR: too many args

    while executing

"run 50000 #50 ps"

    (file "step6.1_equilibration.inp" line 171)

I ran the script again and am waiting for it to be over at least for step 6.1 to check if solving semicolon problem also solves the output of .coor and .xsc and .vel ..

@Chandni Tiwari<mailto:chandni.tiwari_at_monash.edu> Kindly find my configuration file attached.

Thank you all very much.

Best,

Asma Feriel

________________________________
From: Chandni Tiwari <chandni.tiwari_at_monash.edu<mailto:chandni.tiwari_at_monash.edu>>
Sent: April 10, 2020 1:22 AM
To: Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca<mailto:asma.feriel.khoualdi_at_umontreal.ca>>
Subject: Re: namd-l: .coor and .vel output files not generated

Hi Khoualdi,

Please let me know how your configuration file looks like.

On Fri, 10 Apr 2020 at 12:56, Khoualdi Asma Feriel <asma.feriel.khoualdi_at_umontreal.ca<mailto: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

--
Regards
Chandni Tiwari
--
Regards
Chandni Tiwari
--
Regards
Chandni Tiwari

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