[gmx-users] Query regarding water not settled

Mark Abraham mark.j.abraham at gmail.com
Wed Nov 11 15:15:16 CET 2015


The standard advice for this kind of problem can be found here
http://www.gromacs.org/Documentation/Terminology/Blowing_Up. In your case,
you should start by asking what is the expected behaviour for your model
physics, and can you reproduce those properties, before launching your own
research. And update your prehistoric GROMACS version ;-)


On Sat, Nov 7, 2015 at 2:47 PM shalini muralikumar <
vinshal.shalini at gmail.com> wrote:

> I am using gromacs 4.5 version after running a simulation with metal ion
> calcium, water as heteratom and phosphate as a ligand. I am getting an
> error after equilibration steps while running md run too many lincs error
> along with water not settled. What would be an appropriate troubleshoot to
> run my simulation successfully for 10ns. I checked my equilibration step
> for both temperature and pressure and the average was 299.9 k for
> temperature and 1.07 for pressure. During my energy minimization step
> potential energy was -9.07.
> Thanks and regards
> Shalini
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