Umbrella Sampling within a Membrane?

Hello due to the membrane influence is there a method to perform umbrella sampling with membrane coordinates incorporated? I believe not.

Thanks:)

People do umbrella sampling in membrane systems routinely. What problem are you finding, or do you expect to find?

Hello and thank you for your kind update and ok great i just need to then scan the tutorials better to understand this methodology, I will update you accordingly if in need:)

Membranes do require careful consideration, and you may not find a tutorial directly related to what you want to do, but there have been a huge number of posts about such systems via the gmx-users mailing list and many published studies.

Hello and thank you for this kind update and careful direction since the membrane influence is important so I will consider this. I believe Gromacs does not dock a ligand but if gromacs or any other software docks a ligand with membrane included please feel free to let me know which, thanks:)

The typical procedure would be to use docking software (indeed, not GROMACS) to generate the complex and then align the complex within the membrane. I don’t know of any docking software that accepts membranes, because they are not generally relevant for doing docking given the approximations of the technique.

Hello and ok thank you for your kind update:)

Hi Justin I hope you are doing well:),

I am getting closer to my computational investigation, according to our thread after I generate my protein-ligand complex via a docking software outside of Gromacs I was going to run the Gromacs Tutorial 5 Protein-Ligand Complex before aligning the complex within the membrane where I would then umbrella sample. Would you find this methodology of running Tutorial 5 after docking redundant or necessary?

Kind Regards,
Joel:)

You need to generate the ligand topology as in Tutorial 5, but I wouldn’t run an MD simulation in water for a membrane protein (or complex). It’s not possible to simply assign your procedure to any one tutorial, you have to combine concepts and adapt the protocols.

H Justin thank you for your kind update:)

Hi Justin if you know of any transmembrane protein-ligand umbrella simulation studies journaled feel free to refer, I will pubmed search as well.:)

Kind Regards,
Joel

…meaning any particular exceptional ones

@mjsubach
Hello Joel,
Did you find any tutorial on umbrella sampling of membrane proteins, as I am also stuck at the same point?

Thanks.

Hello himanshi09 thank you for your kind inquiry:).

I have docked my ligand to my transmembrane protein and am now in the process of generating the topology for the ligand via Gromacs Tutorial 5, subsequently I will `align the complex within the membrane´ and can then update you accordingly since this would precede the Umbrella Sampling.

Kind Regards,
Joel💡

…and no I have not found this tutorial, in this case you may have to just use different publications etc. which is what im doing.

Hello

Thank you for your update :)

Hi himanshi09 your very welcome:)