[gmx-users] Coarse Grained (Empty space In water)

Kevin Boyd kevin.boyd at uconn.edu
Mon Jun 4 18:58:23 CEST 2018


Why would you want to "ruin" a perfectly good nanoparticle? :)

Could this be a visualization artifact? What kind of treatment of
periodic boundary conditions are you applying prior to visualization?
If you use a PBC option that makes your nanoparticle  contiguous and
not split across periodic boundaries, you would see an empty area in
the box if the nanoparticle is partially out of the box (which would
correspond in size to the fraction of the nanoparticle out of the


On Mon, Jun 4, 2018 at 12:48 PM, Samieegohar, Mohammadreza
<mohammadreza.samiee at howard.edu> wrote:
> Hello
> I am ruining a nanoparticle inside water. I use coarse grained model for water and nanoparticle
> My problem is:
> When I run the system in NVT 298K , after some steps there is a empty area inside the water  (like a hole) while the initial structure has a good distribution for water molecules (P4).
> May you help me to solve the problem ?
> Thanks
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