VMD-L Mailing List

From: hgkrug1_at_gmail.com
Date: Mon Sep 12 2022 - 08:38:15 CDT

Dear All,

Apologies for my inexperience! Diego Gomes <diego.enry_at_gmail.com put
me on the right track. The QM path for Mopac was wrongly specified (in
the "/run/QMMM.conf" and "/run/QMMM-Min.conf" files.

The job runs fine now.

Best wishes
Gert Kruger

On Fri, 2022-09-09 at 10:46 +0200, hgkrug1_at_gmail.com wrote:
> Dear All,
>
> I was able to run the job on a single CPU and I still get the same
> error (log file attached - see: Info: Running on 1 processors, 1
> nodes,
> 1 physical nodes.). 
>
> Any further help will be much appreciated!
> Thanks!
> Gert Kruger
>
>
> -------- Forwarded Message --------
> From: hgkrug1_at_gmail.com
> To: vmd-l_at_ks.uiuc.edu
> Subject: QwikMD QM Tut - FATAL ERROR: Error running command for QM
> forces calculation
> Date: Fri, 09 Sep 2022 09:31:37 +0200
>
> Dear All,
>
> I found a similar error - see
> https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/1005.html
>  
> The (partial) solution there was to run the job in serial (not in
> parallel).
>
> Question then is, how do I change the input for a QwikMD QM
> minimization so that it will only run in serial?
>
> At least it will narrow dowm this issue?
>
> Thanks!
> Gert Kruger
>
>
> -------- Forwarded Message --------
> From: hgkrug1_at_gmail.com
> To: vmd-l_at_ks.uiuc.edu
> Cc: hgkrug1_at_gmail.com
> Subject: QwikMD QM Tut - FATAL ERROR: Error running command for QM
> forces calculation
> Date: Tue, 06 Sep 2022 17:30:58 +0200
>
> Dear All,            
>
> I am doing the Qwik QM/MM tutorial at
> https://www.ks.uiuc.edu/Research/qmmm/Tutorial/Tutorial.pdf 
>
> Everything worked well until the first QM minimization step (page
> 15/16).
>
> I get an Error: FATAL ERROR: Error running command for QM forces
> calculation (error log file - qm.log in th main directory).
>
> I see this problem was reported before: 
> https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0237.html
>  - there was an error with the QM PDB file.  I don't see the same
> issue
> with my QM PDB file?
>
> https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0199.html
>  - no
> solution?
>
> https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2020-2021/0583.html
>  - no
> solution?
>
> A  tar file with setup and run files the that were created so far can
> be found at this link -
> https://urldefense.com/v3/__https://stuukznac-my.sharepoint.com/:f:/g/personal/kruger_ukzn_ac_za/EgII-IBVb9BKju9lBt5zD7cBHxsxl5jf2DEtssZJRwqyCw?e=yDpXal__;!!DZ3fjg!7vWm7Zori4yrFbIA4AtWL7Rj4Vo96j6Bln--RSbsrscbgBfoa2KNjnQ8ZsH8MALZOhnL-jLW5Jk5rK0i$
>
> I have a Dell Inc. Vostro 3670 with a Intel® Core™ i7-8700 CPU @
> 3.20GHz × 12 processor and a NVIDIA GeForce GT 1030/PCIe/SSE2 /
> NVIDIA
> Corporation GP108 GPU card.
>
> Ubuntu 22.04 LTS installed.  For NAMD I have used the binary version
> NAMD_Git-2022-07-21_Linux-x86_64-multicore.tar.gz
>
> When I perform a commandline QM minimization (using the
> "Minimization.conf" file) from the provided tutorial files, I get the
> same error.
>
> I changed the NAMD version on my PC to NAMD_3.0alpha13_Linux-x86_64-
> multicore-CUDA-SingleNode and ran the QM-minimization job from the
> command line again. This gives a different error:  FATAL ERROR: QM
> forces are not compatible with CUDA at this time
>
> The log file is attached (for the last run).
>
> Any kind help will be much appreciated!
> Bets wishes
> Gert Kruger
>
>