[gmx-users] No.of ethanol molecules passing

[Justin Lemkul]

On 12/26/19 7:22 AM, Ali Ahmad (阿力) wrote:
> Hi Groamcs Community
> I am a beginner in gromacs and my work area is pervaporative membrane simulation.
> My queries are
> 1: How to calculate that how many number of "X" molecules (in my case is ethanol) passed through the membrane for certain period of time i.e 1000ps ? from this a graph between No.of molecules "N" vs Time "ns" can be drawn which latter can help to calculate the flux.
> 2: How the trajectories of "X" molecule can be drawn in z-axis "nm" vs time "ns"?
> following is the link of that paper which i am following but unfortunately i can't understand how the author has calculated the things i mentioned above
> https://www.sciencedirect.com/science/article/pii/S0376738817307950

gmx traj -ox -z will give you the z-coordinate of each molecule's COM. 
You can track motion over time and calculate flux that way.

-Justin

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Justin A. Lemkul, Ph.D.
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