Solvating with no overlap

Hello there everybody,
I need to solvate my NP in a box of water. I created the *.psf and *.pdb file for the NP and the water box and followed the procedure here:

https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial—various-tips-tricks

but there’s still water in the gold core of my NP.

Two questions:

° What should I write where it says: [a b c alpha beta gamma} ?

° What should I write where it says: set sel [atomselect $combined “not (same fragment as (exwithin $mindist of solute))”] ?

Thanks, regards

Michele

Hello there everybody,
I need to solvate my NP in a box of water. I created the *.psf and *.pdb
file for the NP and the water box and followed the procedure here:

https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks

but there's still water in the gold core of my NP.

Two questions:

° What should I write where it says: [a b c alpha beta gamma} ?

° What should I write where it says: set sel [atomselect $combined "not
(same fragment as (exwithin $mindist of solute))"] ?

both of those questions are about VMD and not LAMMPS. please choose
your forum wisely.

this is no simple "just do this" kind of answer to your question. you
do need to spend the time to understand how VMD works and particularly
the Tcl script language interface. don't use topotools, if you are not
willing to learn VMD/Tcl fundamentals first.

axel.

Ok, thanks Axel.
Could you suggest me a way to solvate the right way with lammps?

Thanks

Michele

Ok, thanks Axel.
Could you suggest me a way to solvate the right way with lammps?

no. i prefer VMD. i wrote topotools (and the corresponding support
code inside of VMD) exactly for that purpose.

Ok, thanks.
I’ll ask on the proper forums then.

Regards.

Michele

Ok, thanks Axel.
Could you suggest me a way to solvate the right way with lammps?

after reading through the latest commits to the LAMMPS source code
repository. you may now be able to remove overlapping water molecules
now with the delete_atoms command using the very latest sources (i.e.
from today). you still need to merge the two topologies somehow... or
create the nanoparticle from inside of LAMMPS *after* importing the
water box.

axel.