I am trying to simulate a membrane protein in GROMACS. But the system is not getting well minimised. Only if system gets minimized I can do the equilibration step. can anyone help with suggestion?
Probably there's a stearic clash or some other overlap between a protein and the membrane that the minimizer cannot resolve or untangle.
Try Desmond to run your your membrane-bound protein MD. They have an automatic membrane-specific system builder facility, so getting a simulation going, including minimization and lipid equilibration, is really easy.
Agreed. however my suggestion merely reflects the user's knowledge about setting up a membrane systems... based on how the question was asked -- clearly not much. I think there's a benefit for this particular user to skip the details of setting up simulations and just focus on simulation themselves.
I completely understood why you mentioned this, and I agree as well that the question is badly formulated, but if you don't know what you are doing, you shouldn't be doing MD in the first place. Not focusing on the setup is a gross mistake since the setup is what determines what your simulation is going to be.
Membrane protein insertion can be very tricky. I would suggest following a tutorial like this one for system setup with a membrane protein. The g_membed tool might also be helpful.
Their ca be many reasons. those mentioned above are first to be looked at. adjusting the lipids is always tricky. you should have a look at your starting structure. if nothing is obvious consider also that membrane systems are usualy large and may simply need more time to get minimized.
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Hello lavanya, can you please explain your question better? How do you know that the system is not getting well minimized? Which solutions have you tried so far?