Hi all. Well, I'm having a bit of trouble here because the work has decided to go in the direction of something I've never used before with gromacs: dummy atoms (or now "virtual sites").
I've got at least three questions in order to use them: 1 - does the virtual sites need to be included in the .gro files in order to make a simulation run? 2 - do I need to include them in the "exclusion list"? 3 - do I need to include them in the "atoms" section? Thanks a lot in advance for any help anyone can provide in these subjects. ;) Sincerally yours, Jones
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