GROMACS version:
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 .
Thank you very much for the response. However inspite of removing the periodicity i can still see the lower layer of non aqueous solvent diffusing and it appears on top of the SPC water. If i continue with the production run the protien which is placed at 3nm distance from the nonaqueous layer gets pulled upwards by the molecules on the surface of the SPC water. This has been consistently occurring and I am attaching a picture of the simulation for reference. I am using ethylbenzene as the nonaqueous solvent which was packed in a box equilibrated to get the desired density. All the quality control measures were checked and found satisfactory. Then the box was extended along the z direction to include SPC water and the peptide. The system was again minimized and during this step i found few molecules of ethylbenzene on top of the SPC water layer. I continued the equilibration and then the production run. However after about 1ns of the production run the peptde was pulled by overlying ehtylbenzene. I am attaching the snapshot of the simulation for reference and any help would be highly appreciated.
This is still a PBC effect. Where the visualisation box is draw is entirely arbitrary.
From my interpretation of your image, the peptide has one end in contact with the ethylbenzene phase and the other is in the middle of the water phase. You haven’t provided a scale, but from the looks of it the top end of the peptide is too far from the other ethylbenzene/water interface at the top of the image for it to be pulled upwards.
Remember, that both the water and ethylbenzene phases have an upper and lower surface i.e. there are two interfaces. Depending on what you are wanting to do with the simulation, the distance between them may be insufficient. However, nothing appears out of sorts to what would be expected here.
Dear Dr_DBW
Thanks for the prompt reply. The peptide is placed at a distance of 3 nm from the surface of the ethyl benzene layer where the interaction energy between the peptide and surface is zero. The ethyl benzene is of thickness 6 nm and the box length along the z direction 13 nm. So there is a distance of 7nm between the top of the box and ethylbenzene layer. I am attaching another snapshot from another run which clearly shows the interaction with one of ethyl benzene floating at the top of the spc layer. kindly suggest a way
3nm from which interface? Remember, there are two interfaces.
I still don’t see anything out of sorts with this simulation. What do you think is the problem with it?
I would expect the surface of the ethyl benzene phase to sometimes be irregular. You have two interfaces, one is right at the upper/lower box visualisation boundary, the other is 6nm from the lower box visualisation boundary. Every now and then you may get one moving out and separating temporarily. You have a peptide in water with an interface, the peptide will diffuse around in the water and eventually interact with the interface. Both of which from the images you have provided appears to be happening.
Remember, where the box boundary is drawn is arbitrary. The below diagram is also a valid way to visualise your system, you simply move the box boundary around. I think you have a problem that you have some ethyl benzene molecules visible at the top of the box visual boundary? As has already been pointed out, with some tweaking with gmx trajconv you will be able to fix that visual issue.
The entire set up is as shown in the figure. After correction of the periodic boundary condition i should see only the lower interface and not the upper interface which is an image in another box, correct me if I am wrong. My conclusion is that the ethylmolecules has reached the top of the box from the lower layer. My objective is to study the interaction of the peptide with lower interface . During simulation i can clearly see that the peptide is pulled upwards and it is interacting with ethylbenzene molecule at the top of the box. Even the ethylbenzene is seen to be moving towards the peptide from top. Any how i am running the experiment by increasing the box size to 20 nm (Z) and waiting to see whether the effect persists. Once again thank you for sparing time to answer the question.
Again, the visualisation box is entirely arbitrary. Why is it an issue with it interacting with the “upper” interface? Why don’t you want it interacting with it? It is identical to the “bottom” interface. If the peptide happens to go “upwards”, then change your frame of reference and you can perform exactly the same analysis and visualisation as if it went “downwards”. The peptide is going to diffuse around, some runs it may drift “up”, and some it may drift “down”.
Increasing the z-axis dimensions and filling with more water layer will mean it is less likely to interact with the “upper” interface. However, it will still have the same likelihood to “diffuse” upwards from the starting configuration. More atoms (~1.5 times more) will mean it takes longer (probably around 2 twice as long).
