Dear Justin, Thanks for the suggestion, will try to apply position restraints on lipid as mentioned in the advanced trouble shooting section.
Ram On Tue, Sep 22, 2009 at 8:08 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > ram bio wrote: > >> Dear Gromacs Users, >> >> I am following the justin tutorial on KALP-15 in lipid bilayer, I have a >> query regarding the nvt.gro that is after the NVT equillibration phase. The >> mdrun was proper without any warnings or errors, but when i visuallized the >> nvt.gro in VMD, i found that the peptide is intact in between the bilayers, >> but the the two layers got separated or else it is like the peptide bridging >> the the two halves of the lipid bilayer with gap in between the layers and >> also found few water molecules to the sides of the peptide or in the gap >> mentioned betwwn the layers. >> >> Please let me know is the simulation going on normally or there is an >> defect or wrong going on, as the nvt equillibration was proper as i think i >> continued for the next equillibration that is npt for 1ns. >> >> > You shouldn't continue blindly if you get weird results. Please see the > "Advanced Troubleshooting" page (part of the tutorial!), because I > specifically address the issue of a bilayer separating: > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/advanced_troubleshooting.html > > -Justin > > Ram >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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/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/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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/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/mailing_lists/users.php >
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