[gmx-users] density vs time

[Justin A. Lemkul]

nishap.patel at utoronto.ca wrote:

<snip>

> Near the end, the values are fluctuating around one. The reason I was 

That would seem right to me.

> trying to get density values was may be to try an understand if the 
> density computed by gromacs is different for just water system and 
> water+one methane system (i.e. gromacs calculates the density using the 
> box and total number of molecules in the box, which would be fine for 
> water system but for methane+water it would slightly be a little 
> different, no?) and may be normalize my rdf using the difference in the 
> density factor. Does that make sense?

See the manual, section 8.4, for the method Gromacs uses for computing RDF. 
That's the second time I've posted that today.

-Justin

-- 
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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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