[gmx-users] Abot genbox and editcon

[Justin A. Lemkul]

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

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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