It's appeared new question about G_membed Does anobody used this algorithm for insertion of their proteins ? In particular I wounder to know how I can to find optimal parameters ( different scaling factors like in the below command) for insertion in my system( single alpha helix in DMPC bilayer system) and how I can measure area per lipid in the output system?
g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100 James 2011/10/25 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Justin, >> >> I've found the same task of MSU's students :) They simulate membrane >> formation without NPT stage ( after NVT they run production MD). From they >> reports I've found that simplest membrane system could be formed within >> 10-30 Ns. But what about try to make such simulation in vacuum at first >> without any water ? Might the bilayer been formed in such conditions? >> >> Finally I have small question about pereodic boundaries of such bilayer >> system. >> >> E.g I've done simplest system with water consisted of 8 lipid molecules + >> some water. >> This is the representation of the system http://i1209.photobucket.com/** >> albums/cc394/own11/lipids8.png<http://i1209.photobucket.com/albums/cc394/own11/lipids8.png> >> I want to simulate bilayer formation as well as concomitant hydrophobic >> effect ( removing all water from formed bilayer) >> Does the PBC presented in that example ( 2.64196 2.64196 6.85002 for 8 >> lipids) are enought for such lipid movement? It seems that more free space >> aree needed for overal turn of lipid molecules. How I can calculate exactly >> PBC value required for my system ? >> >> > I agree that your system has insufficient space for any real movement > without violating the minimum image convention. Your system must have > adequate room for any lipid to rotate in any direction, and be of sufficient > size to accommodate a formed membrane, which will have dimensions dictated > by the APL for the chosen lipid (and of course, the force field's ability to > produce that value). > > > -Justin > > -- > ==============================**========== > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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