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 <mpi...@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. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists