[gmx-users] gmx solvate

[Alexander Alexander]

Hello Mark,

Thanks for your response.
I know it happens due to overlap, but, just suppose that B and C have
overlap to each other and then due to this some of the B species get
removed, so, why not C removed instead of B in order to get rid of overlap?
Best regards,
Alex

On Tue, May 10, 2016 at 8:52 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

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