From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Jul 30 2019 - 09:16:13 CDT
Please keep CCing namd-l so others can benefit from the discussion or chime in with other suggestions.
A few things about QwikMD and QM/MM. QwikMD prepares as the files to execute NAMD, similarly as a user would run NAMD. Every time that QwikMD runs NAMD, it creates a log file with all print-outs that NAMD produces. So to investigate possible errors, one should check these log files located inside the QwikMD output folder/run. In the particular case of QM/MM simulations, the QM calculation runs inside the folder "run/qmmm_exec/<NAMD conf file name>/<QM region index>". This QM output folder is defined in by the keyword qmBaseDir in the NAMD conf file. Inside this folder, you can also find the outputs of the QM package and check its contents for signs of errors.
QM/MM simulations are in general very slow compared to a "regular" MM simulation, which makes the "Live View Mode" not very useful unless you are running a small QM region with a fast semi-empirical method. You can turn off the (Live View) without preparing the system again by changing "IMDon on" in the NAMD configuration file to "IMDon off".
Now, the error that is terminating NAMD can be due to many reasons including:
- QM package cannot be executed as defined;
- If semi-empirical, the element might not be defined in the package;
- Running NAMD CUDA version. Only the multicore version of NAMD can run QM/MM simulations;
Please inspect the log files to find out what is wrong.
Best,
João
From: 辛志宏 <xzhfood_at_njau.edu.cn>
Date: Monday, July 29, 2019 at 10:06 PM
To: joao ribeiro <jribeiro_at_ks.uiuc.edu>
Subject: Re: Re: namd-l: FATAL ERROR: Must have either an initial temperature or a velocity file
Thanks João,
I installed the latest VMD 1.9.4 alpha and Nightly Build NAMD (2019-07-29), but a new errors occured.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: Error running command for QM forces calculation.
Charm++ fatal error:
FATAL ERROR: Error running command for QM forces calculation.
ERROR) Error connecting to localhost on port 3000
-----Original Messages-----
From:"Joao Ribeiro" <jribeiro_at_ks.uiuc.edu>
Sent Time:2019-07-29 22:03:36 (Monday)
To: namd-l_at_ks.uiuc.edu, "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov>, "xzhfood_at_njau.edu.cn" <xzhfood_at_njau.edu.cn>
Cc:
Subject: Re: namd-l: FATAL ERROR: Must have either an initial temperature or a velocity file
Hi all,
This error is generated by the first implementation of QM/MM simulations in QwikMD. This issue was then resolved, and one can have access to a “fixed” version by using the latest alpha versions of VMD, of by sourcing the QwikMD beta version available at http://www.ks.uiuc.edu/Research/qwikmd/
Best,
João
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov>
Reply-To: <namd-l_at_ks.uiuc.edu>, "Vermaas, Joshua" <Joshua.Vermaas_at_nrel.gov>
Date: Sunday, July 28, 2019 at 2:46 PM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, "xzhfood_at_njau.edu.cn" <xzhfood_at_njau.edu.cn>
Subject: RE: namd-l: FATAL ERROR: Must have either an initial temperature or a velocity file
Add in a "temperature $temperature" line, since that is what the error message wants you to do. I'm a bit confused as to what you mean by the tkconsole, as NAMD doesn't have one. Are you running interactive MD? Putting in commands in the tkconsole within VMD doesn't actually eliminate the error message--B_3647322974_458900729--
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