[gmx-users] Using genbox to REMOVE solvent

Michael Daily mdaily.work at gmail.com
Thu Aug 18 08:32:52 CEST 2011

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?

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