[gmx-users] density vs time

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 16 22:59:19 CET 2010

nishap.patel at utoronto.ca wrote:


> 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 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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