Hi Justin,
Well from the previous post:
The number density for water should be about 32.5 waters per cubic
nanometer. So if my box size is 4 4 4 =64nm^3, then shouldn't number
of water molecules be 64*32.5 = 2080? May be I am not understanding it
correctly. I am using Tip3p water model for my simulations.
Thanks.
Nisha
Quoting "Justin A. Lemkul" <[email protected]>:
[email protected] wrote:
Hello,
I am trying to use genbox to add water molecules to my system
consisting of one molecule of ethane in the box size of 4 4 4nm(
64nm^3). If I understand it correctly, with the system of that
size, I should have ~2080 water molecules in my system, but instead
genbox adds ~2177 molecules of water, with higher density (1018.63
(g/l)). Is that correct?
Should be, but you haven't said what model water you're using.
Assuming SPC, the box you've specified is 10x the size of spc216.gro,
so I would expect that genbox would add roughly 216 x 10 = 2160
molecules, give or take a few. How did you come up with 2080 as the
expected value?
-Justin
Thanks.
Nisha Patel
--
========================================
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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Nisha Patel
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