[gmx-users] Re: questions

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Oct 8 17:40:08 CEST 2013

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



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.

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