[gmx-users] pr_md

[ehab at biof.ufrj.br]

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.
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                             
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> |
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> |
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> >
> >
> >
> >
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