[gmx-users] pr_md

[David van der Spoel]

On Fri, 13 Dec 2002, Luciane Vieira de Mello wrote:

>Dear all,
>
>I am running a pr_md, and got the following message:
>
This doesn't happen to be the CVS version of GROMACS?

If not, did your minimization work out? Did energy converge reasonably
well, are forces < 1000?

>Step 17782, time 35.564 (ps)  LINCS WARNING
>relative constraint deviation after LINCS:
>max 21.626123 (between atoms 2688 and 2689) rms 0.471407
>bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>   2686   2687   51.8    0.1530   0.2187      0.1530
>   2687   2688   89.8    0.1530   0.6611      0.1530
>   2688   2689   89.8    0.1530   3.4618      0.1530
>   2689   2690   89.8    0.1470   3.0238      0.1470
>   2690   2691   87.9    0.1000   0.5723      0.1000
>   2690   2692   87.3    0.1340   0.9661      0.1340
>   2692   2693   60.8    0.1340   0.1681      0.1340
>   2692   2696   61.8    0.1340   0.1693      0.1340
>   2693   2694   50.5    0.1000   0.1501      0.1000
>   2693   2695   54.8    0.1000   0.1592      0.1000
>
>in fact I got this message several times, involving different atoms.
>
>the atoms involved are part of the protein, which should be
>constrain in the pr_md. Shouldn't they not be affected in this step?
>
>Has anyone got a message like this before? it is the first time I am
>seeing it.
>
>cheers,
>+-------------------------------------------------------------------------+
>|                  Dra. Luciane Vieira de Mello Rigden                    |
>| e-mail: mello at cenargen.embrapa.br                                       |
>| Embrapa Recursos Geneticos e Biotecnologia                              |
>| Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
>| PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
>| 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
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>
>
>
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