GROMACS version: 2023.3
GROMACS modification: Yes/No
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Hi all,
I have run md simulations on a couple monomeric proteins. The results are promising but I am wanting to prompt the protein to sample at different maximum dimensions. For example, if the largest residue to residue distance is 100 angstroms in a basic simulation, I would like to do a simulation where the protein is forced to a maximum dimension of 150 angstroms. I am thinking an umbrella simulation may be needed, but I am unsure if this is the right course of direction or how to approach it. I am rather new to gromacs, so I apologize for any confusion. Thank you!
Hi, first of all you should define what “sampling” means to you here. There will be different methods that either quickly provide plausible conformations without (almost) any thermodynamic information, or take a lot of time to yield configurations with more or less reliable Boltzmannian weights. Then there are other considerations - for example, is this protein unfolded/unfolding or just exhibiting an elastic response? Is reversibility important?
Either way though, you might be willing to look at the Plumed interface to Gromacs where you can e.g. define the radius of gyration and run, say, metadynamics on this collective variable.