[gmx-users] About solvation

[Justin A. Lemkul]

vidhya sankar wrote:
> Dear Mark
>                   Thank you for your reply.
>                    I did As u said  But when I visualize  the resulting 
> .gro files in VMD  .The solute molecules are centered (i used the center 
> option in editconf) But solvent molecules are are away . but within the 
> box i need Solute  molecules to be  closely surrounded by  solvent 
> molecules . Is there is Any way to do this ?

If you're limiting the solvation to a finite number of solvent molecules, then 
your box needs to be of the correct size to accommodate those molecules.  It 
sounds like your box is simply too large.

-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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