[gmx-users] About solvation

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 16 18:35:49 CET 2012

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 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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