[gmx-users] water stretched apart

Chetan Mahajan chetanvm10 at gmail.com
Sun May 11 08:09:34 CEST 2014

Dear All,

I need help interpreting one image, that I am sharing via a link:


It's a system of TiO2 crystal ( 2160 atoms, positions restrained with
refcoord-scaling: com), 1 formate ion, 1 sodium ion and 3656 water
molecules, totaling 13133 atoms overall. As you can see TiO2 slab is at the
center of the box. What I am concerned about is the few water molecules
stretched along a long distance (visible via lines) in the snapshot shared
above. Can anyone throw light on what does it mean or why it is happening?
Is it bad totally? Any solution, if it is totally bad?

I am using a timestep of 1 fs for entire simulation.

Thank you very much.


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