Also it is possible that there might be a problem with setting up the membrane. Have you tried running the membrane without protein? -Shay On Sep 19, 2011 3:32 AM, "Justin A. Lemkul" <jalem...@vt.edu> wrote: > > > Michael Daily wrote: >> 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. >> > > An even simpler approach is outlined here: > > http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations#Adding_waters_with_genbox > > It seems to me that the original problem either derives from incorrect > construction, incorrect application of position restraints, or as Mark > suggested, an artifact of PBC. > > -Justin > >> On Sun, Sep 18, 2011 at 5:12 PM, Mark Abraham <mark.abra...@anu.edu.au >> <mailto: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 >> <mailto: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 >> <mailto: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) >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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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