GROMACS modification: Yes/No
Here post your question
In a biphasic simulation as in case of cyclohexane water system, the penetration of water molecules into cyclohexane layer can be prevented by changing the parameter for carbon in vdwradii file. But what I am observing is that few molecules of cyclohexane molecules is seen at the top of the water layer during simulation. Is this normal? During visualization of trajectory of only my protein and cyclohexane for the interaction of my protein with cyclohexane layer I see few molecules above my protein . Is this the molecules diffusing from the cyclohexane layer into the water or is it problem of periodicity. Is there a way to remove this molecules so that I get a clear image .