[gmx-users] How to set the density of the box?

[Justin A. Lemkul]

kecy_wu at sina.com wrote:
>       Hello, I want to set the density of the box (e.g. set 1 g/ml for 
> the water box). I use the density option in the editconf, then use the 
> genbox to generate the box, but the result of the density is not what I 
> setted. How can  I do ?
> 

The density of the box will be governed by how accurate the water model is in 
reproducing experimental values.  As far as I know, there isn't a water model 
that gets density dead on.  You could alter the box dimensions manually and use 
a constant-volume ensemble, but whether or not it's appropriate to make such a 
modification is questionable, since the water models are designed to reproduce 
certain values with certain accuracy.

>       I have another question, I don't find the tip3p.gro and spce.gro 
> water model  in the top file, only have the .itp document. if I want to 
> generate the TIP3P water box, how can I do, or  where can I get the 
> tip3p.gro and spce.gro documents?
> 

You don't need anything special, just coordinates for a 3-point water model and 
sufficient equilibration:

http://www.gromacs.org/Documentation/How-tos/TIP3P_coordinate_file

-Justin

>       Thank you !
> 

-- 
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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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