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
--
========================================
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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