VMD-L Mailing List

From: hgkrug1_at_gmail.com
Date: Fri Sep 09 2022 - 02:31:37 CDT

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!9dGrYmxTDyKmX7az92kww7sV4fcXjhf5jSLJ1ZBbVhhdCusSbqHIinWAjK-JjIe70eqldTpO36e1bFWh$

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