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Hi everyone,
I am recently involved with setting up density-guided simulations in GROMACS (Applying forces from three-dimensional densities - GROMACS 2024 documentation) for a protein-system, and for that I first need to orient the protein (.pdb/.gro formats) along the cryo EM map (in .mrc file format). I have oriented the system accordingly, but while setting up the system for MD simulations, I am facing the following problems:
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Using gmx editconf to insert a PBC box will either translate the protein from its original position (when centered within the box), or will create a box which will not include the protein at all (when the -noc flag is used to prevent the system from translating)
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I was wondering if we need to use the box dimensions from the density data file (obtained from experimental group) instead, but in that case the system will be huge since the box defined in the .mrc file is wayy bigger than the actual system.
I need to generate a pbc box around my protein system in such a way so that the actual coordinates of the protein remains unchanged, but it looks like gmx editconf generates box with respect to the coordinates of the origin. Is there any other way to achieve this?
I would appreciate if someone has some expertise in such setups and simulations, and can provide their valuable feedback.
Thanks a lot for your time!
Triasha
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Triasha Pal
PhD Candidate
Hocky Group
Department of Chemistry
New York University