[gmx-users] pr_md

[David van der Spoel]

On Fri, 13 Dec 2002 ehab at biof.ufrj.br wrote:

>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?
If you do EM do you have constraints turned off? (you should...)

>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         
>> |
>> >+-------------------------------------------------------------------------+
>> >
>> >
>> >
>> >
>> >_______________________________________________
>> >gmx-users mailing list
>> >gmx-users at gromacs.org
>> >http://www.gromacs.org/mailman/listinfo/gmx-users
>> >Please don't post (un)subscribe requests to the list. Use the 
>> >www interface or send it to gmx-users-request at gromacs.org.
>> >
>> 
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> 
>
>
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>