[gmx-users] pr_md

[Luciane Vieira de Mello]

Hi David,

> I'm running the 3.1 version of GROMACS e my minimization work out...but I've
> got the same message of LINCS warning...I'm confuse too.

that is also my case.

Luciane


> Could be something else?
> Thanks in advance,
>
> Elza
> Federal University of Rio de Janeiro
> Biological Physics Lab
>
> > 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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