[gmx-users] gmx solvate

Mark Abraham mark.j.abraham at gmail.com
Tue May 10 20:52:40 CEST 2016


gmx solvate works by considering atomic overlap. You can't get it to
produce a configuration that has overlap (except by setting radii to zero),
and the result seems unlikely to be useful if you did.


On Tue, 10 May 2016 20:09 Alexander Alexander <alexanderwien2k at gmail.com>

> Dear gromacs user,
> As you know, the "gmx solvate" can be used as below to merge two gro files
> which have an identical box size;
> gmx solvate -cp A.gro -cs BC.gro -o ABC.gro
> The A.gro contains only the "A" molecules serving as solute while BC.gro
> contains two types of B and C molecules serving as the solvent.
> Usually, some of the solvent atoms are removed (either B or C or both of
> them) from the final ABC.gro file because of overlapping.
> My question is that how I can  enforce the program to remove only from one
> of the species (for example, B , not from C) if something want to be
> removed?
> Thanks,
> cheers,
> Alex
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