[gmx-users] Insert molecules in system with minimum distance between them

Teemu Murtola teemu.murtola at gmail.com
Sat Oct 3 07:58:00 CEST 2015

On Thu, Oct 1, 2015 at 3:23 PM Justin Lemkul <jalemkul at vt.edu> wrote:

> On 9/30/15 12:15 PM, Ebert Maximilian wrote:
> > I am trying to add n-number of molecules in my prepare
> protein+water+ions box but keep a minimum distance of 1 nm in all
> directions between the newly inserted molecules. On top of that I want to
> replace solvent molecules with the newly added molecules. So basically I am
> looking for gmx genion with the -rmin flag for non ions.
> > Which tool could I use?
> No GROMACS tool will do this.  You can use gmx insert-molecules in concert
> with
> a positions.dat file (with pre-computed locations for the molecules),
> followed
> by gmx solvate.

I extended gmx insert-molecules to this direction in 5165
<https://gerrit.gromacs.org/5165>, which had been in my backlog for some
time now; feedback is welcome (I haven't yet tested the new functionality,
though). The option to control the minimum distance is not there yet, but
should not be technically difficult to add. The biggest question is how
many different minimum distances are required, how would they be specified
from the command line, and how they would interact with the different
distance measures in the tool? At least solute-inserted, solvent-inserted,
and inserted-inserted distances might need different treatment, and then
there are also the van der Waals radii for the atoms that are currently

Best regards,

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