[gmx-users] waterbox

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 11 21:11:19 CET 2010

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?


> Thanks.
> Nisha Patel


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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