[gmx-users] LINCS WARNING - please!

[Bert de Groot]

Luciane Vieira de Mello Rigden wrote:
> 
>  Dear all,
> 
> 
>  I'm doing a new simulation and everything was going fine, till
>  I start the relax_md.
> 
>  Got the following message:
> 
>  Step 0, time 0 (ps)  LINCS WARNING
>  relative constraint deviation after LINCS:
>  max 625001536.000000 (between atoms 5416 and 5418) rms 10529560.000000
>  bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>       62     64   42.8    0.1470   0.2101      0.1470
>       64     65   40.6    0.1530   0.2100      0.1530
>       64     73  113.9    0.1530  12.4138      0.1530
>       73     74  124.7    0.1230  12.4545      0.1230
>  ...
>     8176   8177   90.0    0.1530   0.6303      0.1530
>     8177   8178   90.0    0.1530   0.6087      0.1530
>     8177   8179   90.0    0.1530   0.5895      0.1530
>  Wrote pdb files with previous and current coordinates
>  step 0Segmentation fault
> 
> 


since your problem occurs in step 0 I'd guess that the structure you're
using is not well minimised. Even though the EM itself might have
looked OK (reasonable energies and max force), it might still be that
there is a weird geometry or bump somewhere in the system that the
EM cannot solve (by walking down the gradient). I'd suggest to run
a short MD with a reduced time step (0.1 fs or something), perhaps
with lincs/shake switched off and see where in the structure you
observe a large shift or reorientation (and/or which energy term
shows a large drift or oscillation). That might give you a hint
(and if you're lucky the system might even relax to a configuration
from which you could continue with a normal time step).

--

Bert

ATTENTION: Please note new phone/fax numbers below!

____________________________________________________________________________
Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________