No you can not do that. You can only say that it is drawn at N times
the average number density of solvent molecules. To determine N, find
out the average grid.cube value in a region of pure solvent, let that
value be A, and N=10/A.
Clearly you're trying to do a figure caption, and I'm sorry that the
tool does not do this for you. There are technical issues that make it
harder than you might think to automate although it certainly could be
done.
You can estimate A by sliding the bar in VMD and A is next to where
the bulk water disappears. This will give you an estimate that you can
later use to ensure that your quantitative value is correct. To get
the quantitative value, you'll probably need to run awk over the
grid.cube file and average over a predefined section. Careful though,
don't go all the way to the boundaries of the cube, the corners there
are likely low density due to rotation from trjconv.
Chris.
-- original message --
Dear Chris, thank you for information, they were very enlightening.
Just one more question. Suppose I use an isovalue, say 10, I can
say that the drawn surface is 10 times the average number density of solvent
molecules? I am using -div option.
Bests
eef
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
