Dear Tsjerk, I was afraid that it works like this... It is possible to "center" the system in a different way? without this additional component to the water displacement? What I want is to have protein always in the center of my view But not by some artificial "centering" inside the box nor changing the coordination system, just by choosing from pbc those water molecules which are around protein even though protein is passing through box edge. So my box would be drifting with protein but coordination system is fixed somewhere outside the box. I am not sure if I make it more clear ;) Thanks! Best!
tomek On Fri, May 6, 2011 at 10:28 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hey :) > > Option -center shifts the system, which will show up as a component in the > displacement. > > Cheers, > > Tsjerk > > On May 6, 2011 5:39 PM, "Justin A. Lemkul" <jalem...@vt.edu> wrote: > > Tomek Wlodarski wrote: > > Dear Justin, > > Thanks, sure I will give more > details. > > This comman... > > Are all the measurements being done in VMD, or are you using g_dist for any > of these? If you're using g_dist, then some of the distances may be > affected by using your old .tpr file, wherein the protein is perhaps not > centered. > > If all of the measurements are being done in VMD, then I can't comment, but > perhaps someone else can. It might be useful to show how you're doing these > measurements. If you're not using g_dist, it would be interesting to see > how the results of g_dist and VMD compare, in order to tease out the source > of the difference. > > -Justin > >> Best! > > tomek > > On Fri, May 6, 2011 at 1:15 AM, Justin A. Lemkul >> <jalem...@vt.edu> wrote: >>... > > -- > 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 > -- 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