Simulation of water

User discussions
1

GROMACS version:5.1.2
GROMACS modification: Yes/No
Hi,
I have completed the simulation of only water molecules. I want to calculate the g(r) between oxygen and hydrogen atoms. How I create the index file and calculate the g(r)?

With Regards,
Chinmay

2

Use gmx make_ndx to create separate groups for the O and H atoms, then select them when prompted by gmx rdf.

3

Screenshot (16)
Screenshot (16)1920×1080 162 KB

Dear @jalemkul sir,
I got the following graph. Is it correct?

Thank You
With Regards,
Chinmay

4

For the given OW-HW selection, yes, but it is dominated by the intramolecular (bonded) interactions. Normally one is most interested in OW-OW and HW-HW RDFs to understand the structure of the liquid.

5

Thank you sir