[gmx-users] Using genbox to REMOVE solvent

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 18 08:54:26 CEST 2011

On 18/08/2011 4:32 PM, Michael Daily wrote:
> 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?


One way to test your hypothesis is to strip the waters from POPC, 
resolvate it with the right atom size, change it to POPE, solvate the 
previously-solvated structure and see if more waters get added. Now 
they'll be in a contiguous lump at the end of the .gro file.


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