[gmx-users] LJ interactions in gromacs

[Kevin Boyd]

Hi,

A few groups have done things like this to shape membranes. See
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700167/
and
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00765

I was involved in the second publication, so feel free to contact me about
implementation details if they're unclear.

However, I'm not sure that this approach is reasonable for excluding lipids
from a protein cavity. What else is supposed to occupy that cavity? A
vacuum is unphysical, and if it's a part of the protein that's embedded in
the membrane you don't want it filled with water. It also seems like this
could lead to perturbations of the annular lipid shell, which may or may
not be important.

Kevin


On Sun, Feb 16, 2020 at 3:42 PM 凌未风 <grx1985 at qq.com> wrote:

> Hi,
>
>
>
> I have a technique problem I would like to ask for suggestions.
>
>
>
> I would like to include some dumb atoms in my simulations. These dumb
> atoms only have LJ interactions with some atoms in the system (e.g., the
> lipid tails ), but do not interact with the other atoms (e.g., protein,
> waters). Is this possible in gromacs? If so, how could I do that?
>
>
> The reason I want to do so is that, I am simulating a membrane protein in
> a bilayer, and the lipids sometimes come into a cavity of the protein
> (which is what we do not want to happen). I want to fill the cavity with
> dumb atoms, so that the lipids will not come in.
>
>
>
> I am really appreciate for any suggestions. Thanks in advance for your
> help.
>
>
>
> With my best regards,
>
> RXG
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