[gmx-users] Re: LINCS Warning using mdrun

Steffen Wolf swolf at bph.rub.de
Tue Mar 14 16:12:08 CET 2006

> -----------------------------------------------------------------------
> Hi
> I used the initial minimization run using grompp and mdrun using 
> steepest descent for 400 steps and 0.002 ps as the step size. The 
> constraints are all-atom.
> The following is the output from the log file that was generated after 
> the md.
> Any suggestions?
> Thanks
Was the system already completely munimized, i.e. has it reached 
convergence? 400 steps seems a bit small to me. I usually had problems 
with the constraints when the system had some kind of "point of frition" 
where a bad contact was still existing. Did you check which where the 
atoms mentioned by the lincs warning or if there were bad angles or 
contacts in the starting structure?
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum

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