[gmx-users] Lennard-Jones Wall ( help please ! )

[Lamm Gro]

Dear Mark ,

Thanks for you reply .

Regards,
Saeed.

On Thu, Dec 1, 2016 at 2:05 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> I asked Berk Hess, who has some experience here, and he suggests:
>
> The 1 nm for wall-r-linpot is far too long. That creates a linear, very
> weak, attractive (!) wall potential. This should be 0 or much smaller than
> the LJ sigma.
> But maybe you already tried that. In that case you should energy minimize
> (better) before running MD.
>
> Mark
>
> On Wed, Nov 30, 2016 at 1:21 PM Lamm Gro <lammgro at gmail.com> wrote:
>
> > Dear Gromacs users ,
> >
> > I am new in Gromacs and I joint to mailing list recently .
> > unfortunately no one answered my question about lennard-jones wall .
> > Can you please help me about that ?
> > I want to use two lennard-jones walls at special distance from each other
> > at Z direction but I don't know how I can do that by gromacs .
> >
> > I used
> > ...
> > pbc                      = xy
> > nwall                    = 2
> > wall-atomtype      = opls_740 opls_740
> > wall-type               = 9-3
> > wall-density           = 50 50
> > wall-r-linpot            = 1
> >
> > But I get lost atom error , I think it's because of some atoms that are
> > beyond wall !
> > Can you please let me know How i can change the wall location in system ?
> >
> > Thanks in advance .
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