Water Substrate Simulation

I’m trying to create/initialize a water drop on top of a number of graphene layers, but I’m having trouble
getting the initial geometry created.

I’m finding/modifying lammps data files for either the substrate and the water, but both separately, and lammps has issues with creating lattices, regions etc after a read_data command.

My route to getting this done which I’m trying right now is inputting a water.pdb file, and a graphene.xyz file separately into vmd, and using the topotools plugin to
merge both of these geometries and to create a lammps data file for the combined water and graphene layers.

Is this a sound idea?
guidance appreciated

very respectfully,

I know this is a help-list for lammps not vmd.

I'm finding/modifying lammps data files for either the substrate and the water, but both separately, and lammps has issues with >creating lattices, regions etc after a read_data command.

You can only read a data file once, but there is no inherent problem
with defining regions, lattices, or using create_atoms after
reading a data file. But for a complex system in close
contact you are probably better off creating one data file
as a pre-processing step.

Steve

Thanks.

I'm trying to create/initialize a water drop on top of a number of graphene
layers, but I'm having trouble
getting the initial geometry created.

I'm finding/modifying lammps data files for either the substrate and the
water, but both separately, and lammps has issues with creating lattices,
regions etc after a read_data command.

My route to getting this done which I'm trying right now is inputting a
water.pdb file, and a graphene.xyz file separately into vmd, and using the
topotools plugin to
merge both of these geometries and to create a lammps data file for the
combined water and graphene layers.

Is this a sound idea?

yes, very much so. you just have to make sure
your atom types/names/labels don't overlap.
i've written the precursor to topotools to set up
the calculation for this animation, for example.

http://www.youtube.com/watch?v=_iRo_UNHgrw

cheers,
     axel.