Unfortunately genbox will put waters anywhere there is a space, including inside the membrane. This can easily be fixed by making a script to remove waters that are z +/- ~2 nm from the membrane center (you should run g_density on the system to figure out the optimal distance filter). You can run this after running genbox.
On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 19/09/2011 9:42 AM, Sweta Iyer wrote: > > Hi, > I embedded my protein of interest into a DMPC membrane by the g_membed tool > with the following command: > g membed -f input.tpr -p system.top -n index.ndx -xyinit 0.1 -xyend 1.0 > -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100 > > I then energy minimized the resultant structure for 1 ns before the > position restraint dynamics and the productive run. > My structure looks fine after the em. However, when I do the PR and look at > the structure it looks weird in that half of the protein is hanging out of > the membrane and there seems to be a patch of water molecules that seem to > have entered the membrane. > > I have no clue what must be possibly going wrong here. Should I have > equilibrated the system for longer than 1ns or is it something wrong with > the membrane insertion. > > > Sounds like the advice here might be useful. > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > Mark > > -- > 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 > -- ==================================== Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison)
-- 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