[gmx-users] LINCS warnings for O-P-O-H bond

[Luciane Vieira de Mello]

Dear all,

I've added a singly negatively charged phosphoserine to my GROMACS
dictionary.   All seemed well and the MD runs.  What worried me now are a
series of warnings e.g.

Step 4162, time 0.8324 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 0.000717 (between atoms 603 and 604) rms 0.000010
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    603    604   30.0    0.1000   0.0999      0.1000
step 4170, will finish at Tue Feb 11 13:46:38 2003

This bond is my O-P-O-H bond in the phosphoserine.  I uncommented the
following line in the ffgmxbon.itp file

    P   OA    1     0.000       1.046      3

Is this right?  Or do we not need to worry about a dihedral for
A-B-C-hydrogen?

Another strange aspect is that it is taking more than a overnight to run
20ps, what usually takes a couple of hours.

Thanks for your help

Luciane


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|                  Dra. Luciane Vieira de Mello Rigden                    |
| e-mail: mello at cenargen.embrapa.br                                       |
| Embrapa Recursos Geneticos e Biotecnologia                              |
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