Hi all, I am looking for a relatively easy way to make minor modifications to a solvated system in gromacs without having to replace the whole solvent layer. Specifically, I'm swapping out some molecules (technically, just swapping residue and atom names) in a MARTINI model and I think this causes clashes with the first solvation shell if I increase the size of the headgroup (e.g. POPE -> POPC). So what I want to do is simply find any solvent molecules that have severe clashes after this modification and remove them - I know genbox checks for overlaps in this way when initially solvating a system, so is it possible to make it check for and remove such overlaps in an EXISTING system?
Thanks, Mike
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