[gmx-users] Water molecule cannot be settled

Marcos Villarreal arloa at dqb.fcq.unc.edu.ar
Mon Oct 27 14:24:01 CET 2003

On Monday 27 October 2003 07:59, you wrote:
> I have been attmpeting to perform both steepest descent energy minimisation
> and MD upon a DMPC lipid bilayer containing water molecules.
> At each attempt I am confronted with the same error message which is:
> water molecule at position "X" cannot be settled, check for bad contacts or
> reduce timestep. (X being an integer)
> This has been reported at both timesteps of 2fs and 1fs and I have removed
> all water molecules from the pdb file that appear to be in unstable
> environments (i.e. inside or close to the bilayer area). Is there any other
> procedure possible to correct this problem?

You can try the minimization with fully flexible molecules
(#include "flexspc.itp"  for water in .top, and constraints  = none   in .mdp)
and decrease emstep (in .mdp) to something like 0.001


Marcos Villarreal
Grupo de Biofisica
Departamento de Quimica Biologica - CIQUIBIC.
Universidad Nacional de Cordoba.
Cordoba. Argentina.

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