[gmx-users] gmx solvate

[Mark Abraham]

Hi,

If a given B has an atom that overlaps with A, it gets removed. If a given
C has no atom that overlaps with A, it doesn't get removed. If your input
has B and C that overlap then you have bigger problems to solve first.

Mark

On Tue, May 10, 2016 at 9:31 PM Alexander Alexander <
alexanderwien2k at gmail.com> wrote:

> 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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