In gromacs while performing membrane protein simulations, it is taking much time to complete mdrun step as the protein system is huge, so I want to ask, is there a procedure which can be implemented so that we simulate just the region surrounding our membrane protein? lipid bilayer used is DPPC512 and force field being used is gromos54a8_lipid.ff.
Thank you in advance.
Are you saying that you want to remove lipids that are away from protein ? If then chose a rectangular box containing the region of interest and remove all other particles.
Dear Divya Jhinjharia ,
I do not know the size of your protein, but depending on the molecular behavior you are trying to observe, you can always try a coarse-grained force field, such as Martini. A coarse-grained force field will dramatically diminish your system size, allowing you to run it more smoothly on your machine.
But this approach heavily depends on your research question.
Best regards,
Bruno
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