Hi Lina, Don't combine fitting, centering and pbc options. It may not work as expected. That's why the workflow is given. Use separate passes. By the way, first centering on the protein followed by putting molecules in the box should also work.
Cheers, Tsjerk On Oct 28, 2011 9:01 AM, "lina" <lina.lastn...@gmail.com> wrote: On Fri, Oct 28, 2011 at 12:34 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Lina, > > Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump > > Hope it helps, Hi, Thanks. I tried trjconv_g -fit translation -pbc nojump, ideally it should work. but still not, after I tried the minidist, I noticed the peak around 270ns, I attached the figure, what's the possible reason for this distance? Thanks, P.S the box dimension 6.21279 6.21279 6.21279 > > Tsjerk > > On Oct 28, 2011 6:27 AM, "lina" <lina.lastn...@gmail.com> wrote: > > On Fri, Oct 28... > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/g... -- 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
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