[gmx-users] pr_md

[Luciane Vieira de Mello]

Dear all,

I am running a pr_md, and got the following message:

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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