[gmx-users] waterbox

[Justin A. Lemkul]

nishap.patel at utoronto.ca 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
> 
> 

-- 
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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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