[gmx-users] RDF

[mah maz]

Thanks Justin! I cant find so much details in the manual; there are only
general facts. does g_density give partial density?


On Mon, May 18, 2015 at 11:25 AM, mah maz <mahmaz71 at gmail.com> wrote:

> Hi Justin
> The fact is I want to calculate water density in the system. If I select
> group1: oxygen and group2: oxygen, g_rdf command gives me very large
> numbers. Is it the number of atoms that should be changed to g/cm3?
> Besides, what does it calculate, each O is a reference atom during
> calculation?
> Thanks a lot!
>
> On Sun, May 17, 2015 at 2:17 PM, mah maz <mahmaz71 at gmail.com> wrote:
>
>> Dear all,
>> I want to calculate the radial distribution function of water molecules
>> in my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers
>> which is not logical I suppose. Is it meaningful if I separate oxygen and
>> hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is
>> reference atom necessary to get RDF?
>> Thanks!
>>
>
>