[gmx-users] Switch box type

[Mark Abraham]

You'll have to re-equilibrate anyway, so I wouldn't bother trying to keep
any solvent.

Or follow the same instructions and recognize that you have a cluster of
solvent+solute that you wish to keep whole, and so will need an index group
that recognizes that.

On Sun, Feb 17, 2013 at 3:32 AM, Yun Shi <yunshi09 at gmail.com> wrote:

> Hi all,
>
> I did conventional MD of a protein in solvent in a dodecahedron box
> for 60 ns, and now I want to take the end structure (protein with a
> shell of solvent in close proximity with the protein at 60ns) and put
> it into a rectangle box for SMD simulations. I used g_select on the
> original trajectory without any pbc manipulation.
>
> But I was not able to convert the MD end structure into the right
> representation by trjconv and editconf: although it is easy to make
> the protein whole, the solvent shell seems to always sit partially to
> the edge of pbc box. I first tried "Suggested trjconv workflow" from
> gmx website, and then tried trjconv -pbc nojump/ atom/ mol, -tranlate
> x y z, -center etc., and related flags in editconf.
>
> Can someone suggest another workflow of doing this?
>
> Much appreciated.
>
> Yun
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