[gmx-users] waterbox

[nishap.patel at utoronto.ca]

  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" <jalemkul at vt.edu>:

>
>
> 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
>>
>>
>
> -- 
> ========================================
>
> 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
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536