[gmx-users] bad contacts and/or reduc

[Tsjerk Wassenaar]

Hi Davood,

Although there could be many causes, in this case I'd suspect that there is
a water molecule trapped inside the protein. This can be the result of
solvation using genbox. An isolated water molecule can start to "rattle". It
will get close to one side of the microcavity and "kicked" to the other
side, where it will be overlapping more and "kicked" back even harder. This
process can repeat itself until the overlaps can't be solved anymore and the
system blows up, typically telling you the water molecule couldn't be
settled. Check for isolated water molecules and delete them from the
structure file if necessary.

Hope it helps,

Tsjerk

On 5/27/06, davood ajloo <ajloo2000 at yahoo.com> wrote:
>
> Dear gmx-users
> We want to study interaction of ligand to enzyme. We constructed the gro
> and top file from Prodrg and add it to the end of enzyme gro and change the
> number of atoms. Some of calculation carried out until mdrun of pr.mdp,
> but in this step we encontered to following error. what is the cause of it
> and how we can solve it.
> Thanks a lot of.
>
> tep 5, time 0.01 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 0.007443 (between atoms 3555 and 3557) rms 0.000281
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     506    507   30.0    0.0999   0.0999      0.1000
>    1861   1862   37.0    0.0999   0.1000      0.1000
>    2131   2132   30.4    0.0999   0.0999      0.1000
>    2604   2605   35.4    0.0989   0.0997      0.1000
>    2997   2998   36.5    0.0999   0.1000      0.1000
>
> t = 0.010 ps: Water molecule starting at atom 12011 can not be settled.
> Check for bad contacts and/or reduc
>
>
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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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