Hi every body
I want to simulate gas absorption with gromacs.
I have a box with three part , amine and water in the middle of box and gas is around of it(gas+amine solution+gas). Firstly I equilibrated the amine solution in npt ensemble . Then in special density , I made the gas box. I matched them together .
I want to calculate diffuse coefficient of gas in amine solution and I want to see rdf C (co2) and N (amine) .How can I see diffuse coefficient change in z direction like the picture attached? And I want to calculate diffusion coefficient of gas in amine solution part ( I want to examine the gases that have penetrated into the amine for result) and then use msd and rdf for that gas molecules.How how can I do this?
thanks for your answers
Dear Afsane
You could use msd analysis in different place of your simulation box which is determined with an index file
gmx msd -d md.xtc -s md.tpr -n index.ndx -o msd.xvg
You could use rdf analysis to find the radial probability of finding carbon dioxide around amine molecules. for example, the probability of finding carbon atom of carbon dioxide around the nitrogen atom of the amine
gmx rdf -f md.xtc -s md.tpr -n index.ndx -o rdf.xvg
Hope it helps
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