[gmx-users] Group vs Verlet pair-lists

leila salimi leilasalimi at gmail.com
Wed Jul 16 20:29:14 CEST 2014

Dear GROMACS Users,

I have a question regarding the Neighbor searching, I used group scheme
when I used 4.5 and now I found that there is verlet in version 4.6. When I
compare the trajectories, For verlet simulation I found that the atoms of
water molecules are separated and it caused the long bond in vmd. I mean
that one hydrogen is located on the right side of the cell and the oxygen
and another hydrgon are on the left side that the first hydrogen can come
with periodic image, but these long bond (artifact bonds) are not
convenient and it is difficult for visualization.

I did not have this problem with previous method (group). Could you explain
me what it is happened in  Cut-off schemes = verlet?
And is it possible to have the trajectory with the right bonds (not broken

Kind Regards,

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