Re: NAMD-QM/MM TUTORIAL: Atoms moving too fast error

From: M. A (
Date: Fri Nov 22 2019 - 09:43:20 CST

Hi Marcelo

Thank you very much for your guidance and fortunately, it worked great. As
you suggested, I used the latest version of NAMD and my problem was solved.

best regards

On Mon, Nov 11, 2019 at 7:21 PM Marcelo C. R. Melo <>

> Hi Maryam,
> This is probably an issue of incompatibility between an older version of
> NAMD and the latest version of MOPAC.
> MOPAC recently changed the way it write output files, so please make sure
> you download the "nightly build" version of NAMD. This version has an
> update that allows it to read the new MOPAC output file format.
> Please let me know how that works for you.
> Best,
> Marcelo
> On Sun, 10 Nov 2019 at 04:53, M. A <> wrote:
>> Dear All,
>> I want to execute QM/MM simulation through QwikMD plugin of VMD. For the
>> first step, I tried to do NAMD-QM/MM TUTORIAL. First MD and
>> equilibration were done completely but at the QM/MM part, the minimization
>> step was done completely but at the annealing part I faced this error:
>> ERROR: Atom 2575 velocity is 3.75515e+10 -2.86311e+09 9.02613e+09 (limit
>> is 24000, atom 333 of 672 on patch 37 pe 0)
>> ERROR: Atom 69449 velocity is -2.36584e+09 1.80383e+08 -5.68667e+08
>> (limit is 24000, atom 628 of 672 on patch 37 pe 0)
>> ERROR: Atoms moving too fast; simulation has become unstable (2 atoms on
>> patch 37 pe 0).
>> for knowing whether my files have a problem or not even I used ready
>> minimization output files of the tutorial, but again I faced this error.
>> I would like to know if anyone knows how to solve this problem?
>> Could this error be because of my MOPAC file and its installing process?
>> best regards
>> Maryam
>> --
>> Maryam Atabay
>> Nano Computational Chemistry. Ph.D.
>> Department of Physics, Sharif University of Technology

Maryam Atabay
Ph.D in Nano Computational Chemistry
Department of Physics, Sharif University of Technology

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