[gmx-users] crystal slab and position restraints: com option

Chetan Mahajan chetanvm10 at gmail.com
Sun May 11 19:52:01 CEST 2014

Dear All,

I am new to GROMACS. I am simulating TiO2 crystal slab (2160 atoms, slab
dimensions:  30.63 A0 x 37.76 A0 x 21.05 A0) solvated by 3656 water
molecules, 1 sodium ion and 1 formate ion. I am applying position
restraints to each Ti and O with refcoord-scaling: com. With com option, we
expect crystal to not change in dimensions, but my crystal slab dimensions
after equilibrium and production runs are 29.82 A0 x 35.91 A0 x 19.52 A0.
So we see that slab has shrinked. Is this okay?

Thank you very much.


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