[gmx-users] Abot genbox and editcon

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 17 17:55:37 CET 2012

vidhya sankar wrote:
> Dear justin Thank you for your previous reply
>                                               I have solvated  my 
> protein molecule with specific number of water molecules By keeping the 
> protein (solute) at center of box (option available in editconf)  but 
> when i visualize the resultant  .gro file in VMD  the solute molecule 
> are not closely surrounded by  water molecules i need Solute  molecules 
> to be  closely surrounded by  solvent molecules  without changing the 
> dimension of box i am using Cubic box is there is any option in 
> available in gromacs

No - genbox works by tiling the given solvent coordinate file into the solute 
coordinate file starting at the coordinate origin.  You could randomly insert 
individual water molecules with -ci -nmol, but you'll still end up with 
significant voids akin to the gas phase, or more likely something that doesn't 
even make sense.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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