Membrane Bilayer Box Size and Solvation

User discussions
1

GROMACS version: 2019
GROMACS modification: No

Hello all.
My aim is, model a bilayer membrane from CHARMM-GUI, equilibrate the asymmetric mixed bilayer and use the final frame for drug-membrane interactions studies. As of now, the first step is done, and now drug-membrane interactions studies.

Issue 1: PBC-centered membrane structure has lipid tails projections, out of the PBC box. I added the drug and increased the box size in the Z direction alone (6.60073 X 6.60073 X 11 nm^3). [XY dimensions are taken from the previous equilibration step and preserved the same]. Deleting those lipid molecules seems not good because there are only 25 LipidA are in the upper leaflet and it will affect the similar surface area in the upper and lower leaflet. Or if I increase the box size in XY direction, water will be there on either side of lipid tail projections, but the literature never mentioned such a water padding method (as per my knowledge). Are these projections are normal or allowed? I hope it will create issues during tpr generation and energy minimization if I keep the same. How to solve this?

Issue 2: As per Researchgate answers, I increased the “C” vdw radius (temporarily) during solvation, so that water will not be placed inside the bilayer hydrophobic packing. Is it a proper way to perform during the solvation to avoid water permeation? If this is acceptable, what is the proper “C” vdw radii to consider, avoiding dehydration?

Kindly provide me your valuable suggestions.
Thanks for reading.

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2

Hi,

point 1: I assume that you use periodic boundary condition, thus your box is surrounded by 26 image of the real box. In VMD using the menu option graphics → representation → periodic you can visualize all the 26 image of the box. The lipids are in the box, but each lipid is visualized as whole, such visualization give the impression they are outside the box. Please note that you have a vacuum area in the box shown in the figure, check that it is really what you want.

point 2
I guess the suggestion is only for building the starting structure of the solvated system and not for running the simulation.

\Alessandra

3

Thank you so much for your reply, above two of my doubts are solved. I can able to run simulations for my drug-membrane systems, without any errors. The process is clear and understandable.