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