[gmx-users] water stretched apart
tsjerkw at gmail.com
Sun May 11 08:31:07 CEST 2014
That's due to PBC. Use trjconv -pbc whole to fix it.
On May 11, 2014 8:12 AM, "Chetan Mahajan" <chetanvm10 at gmail.com> wrote:
> 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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