From: Dudas, Balint (
Date: Thu Jun 14 2018 - 04:31:18 CDT


Thanks for the answer it seems that it was the problem. Now I am just facing a new kind of problem, running this tutorial - in which there are only +-23 000 atoms I get an error message: "Memory allocation failed on processor 0". This was not the case when using the same setup for MM only...

Do you know what the problem might be?

From: <> on behalf of Fotis Baltoumas <>
Sent: 13 June 2018 11:09:35
To: Dudas, Balint;
Subject: Re: tutorial-l: NAMD-QM/MM: "QM forces are not compatible with CUDA at this time"


I think the error is pretty much self-explanatory. The QM/MM interface is not compatible with CUDA yet, therefore the CUDA-enabled version of NAMD will not run.

The matter can be easily resolved; simply compile a second NAMD version without CUDA support (i.e. using only CPUs) and use that. Or download one of the precompiled distributions if you're in a hurry.

Just a note, the version you say you have is not 2.12, it's a nightly build with newer features, that will eventually become version 2.13. So I would advise you to consult the nightly build's user guide for more information (> ). Although, from a quick glance, I see that they still haven't included the QM/MM code in the guide yet.


On 13-Jun-18 12:42, Dudas, Balint wrote:

Dear All,

I'm trying to go through the 'NAMD-QM/MM' tutorial and have already got to the point where I prepared (with the help of QwikMD) the inputs for the QMMM-Min simulation. Once I load it into QwikMD and launch the 'Start Minimization' simulation (and select the number of CPUs to use and set up the namd2 executable path - which worked perfectly without the QMMM before) it returns with a FATAL ERROR message. In the .log file everything works until the point where QMMM is needed. There I get the message:

"FATAL ERROR: QM forces are not compatible with CUDA at this time".

I'm using a version of NAMD: NAMD_Git-2018-06-13_Linux-x86_64-multicore-CUDA (2.12). MOPAC has been installed and CUDA-5.5 has been set up for. The same error message occurs when using ORCA instead of MOPAC so I guess it is independent of the QM software applied.

Could anyone help what the problem might be?

Fotis A. Baltoumas, Bsc, Msc
Phd Candidate, Bioinformatics Postgraduate Programme
Section of Cell Biology and Biophysics
Department of Biology
National & Kapodistrian University of Athens
Panepistimiopolis, Athens 157 01, GREECE
email :<>
Tel.: +30 2107274876
Mob.: +30 6979258570
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