Gavin Melaugh wrote:
Hi all
I have a system of 40 solute molecules in a solvent of 480 crown ether
molecules. I am not trying to insert 100 methane molecules into this
relaxed and well equilibrated structure using genbox.
There are clearly visible cavities in the fluid but genbox only alllows
the insertion of 8 methane molecules. How can I circumvent this problem ?
The command I use is
genbox -cp test.gro -ci methane.gro -nmol 100 -try 5 -p combined.top
where combined.top includes all three itp files, and test.gro is the
initial solute and solvent configuration.
You might try reducing the value used for -vdwd in genbox, or otherwise
shrinking the vdW radii in vdwradii.dat, but be warned that if you have to
finesse the system too much, likely any resulting simulation will be extremely
temperamental, if you can even get it to run.
-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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