[gmx-users] Re: questions

[Tsjerk Wassenaar]

Dear Dwey,

Please direct questions like this to the gromacs user list, after asserting
that the answer has not already been given. In addition, please read
http://md.chem.rug.nl/~mdcourse/molmod2012/md.html

Regards,

Tsjerk


On Tue, Oct 8, 2013 at 5:35 PM, Dwey <mpi566 at gmail.com> wrote:

> Dear Tsjerk,
>
>    I saw a discussion related to "solute at the center" on gmx-users.
> (See
> http://lists.gromacs.org/pipermail/gmx-users/2011-October/065292.html)
>
> I have similar issues of centering a protein in water.  After I add
> water into a box of dodecahedron, water did not cover the whole
> protein and protein is NOT placed in the center of water, although
> protein indeed is located in the center of box.
>
> like
> editconf_mpi -c -f protein.gro -o protein_box.gro -bt dodecahedron -d 1.2
>
> ( Note that increasing a box size is not an good option because it
> will take more much time in MD production)
>
> See the resulted image attached
>
> Base on previous discussion, I wonder if you can help me center the
> protein in the water.  ( I already tried commands many times like
> trjconv and editconf but in vain)
>
> Please kindly advise.
>
> Many thanks.
> Dwey
>



-- 
Tsjerk A. Wassenaar, Ph.D.