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

From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Mon Nov 11 2019 - 09:50:36 CST

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 <matabay2010_at_gmail.com> 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
>
>

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