GROMACS version: 2023
I am new to GROMACS and want to simulate ligand-protein complex using lipid bilayer model. Is the DPPC model available for this version. I’m a bit confused. Please help
Dear @priya_0507 ,
The lipid bilayers are not related to GROMACS version, but to what force field you want to use (which, to some extend, may be limited by the software you want to use).
You want to simulate DPPC and a ligand-protein, so you can user AMBER, CHARMM36m, GROMOS, MARTINI force fields etc, it really comes down to the level of detail you want. I can guess you may want to use all-atoms simulations, but this really comes down to the system you want to study.
However, given this question of yours, I feel like you are very new to this kind of simulations and on what they do relay. I encourage you to go through this suite of tutorials, specifically the first, the second and the fifth. They can really help you figure out what is this about and to better tune your focus for your research. Hope this helps! :)
Hi obZehn, thank you so much for your response.
I’m really afraid of this gromacs and I’m unable to do for my fear. I don’t have anyone who can help me in this regard.
May I request your help in my learning of GROMACS. Can you please help me with your time and help me learn this for 1 or 2 days. Please don’t take me wrong, I can pay you fees for this tutorial.
Requesting your help.
Hi @priya_0507
This is not really my job (I am no expert in ligand binding simulations) nor I have the competence to be a decent MD teacher. However, the main point here is that in one or two days you can’t cover much. A proper (at least sufficient) understanding of MD requires some statistical mechanics, some computer science, and some specific knowledge regarding your field, e.g., the basic bio-chem information and understanding of your ligand/protein systems. If you plan on running yourself these simulations, to be able to prepare such systems and to have insight on the analysis, especially if you plan on doing enhanced MD with free energy estimations for ligand binding, then the training will require months (if not years, we are talking PhD level science at least), as these are proper research fields. There are a few very nice tutorials that can help you getting some grasp of the science behind MD from GROMACS official people (here) and other top notch experts (like here). However, I feel like you really have to work out what is your research question and if it is worth using MD even before starting to think about running simulations. If you already know that spending time on MD is worth and required and you need specific expertise on these systems fast, then my best suggestion would be to find an already expert computational partner for your research, as you risk spending time and getting garbage results since these systems are notoriously hard to characterize and study.