Thank you Justin.
On Mon, Jun 9, 2014 at 5:28 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/9/14, 3:22 AM, 陈功 wrote: > >> Dear Venkat, I guess there are some other methods to generate new lipid >> bilayer construct by using genbox -cp your_membrane_protein -ci >> lipid_monomer >> -nmol xxxcalculate by yourself -try 1000 -cs solovents.gro -p top.top -o >> new_conf.gro or using editconf & cat ...Another way, you can try the >> script >> packmol. Be more patient. haha, I m also a new gmx user. Good luck, chen >> > > Packmol is a good choice, but the approach above with genbox likely won't > work. It will produce a random insertion of lipids. The simplest way > within Gromacs to create a membrane of sufficient size is to place the > protein in a suitably sized box (with editconf) and then > > genbox -cp protein.gro -cs membrane.gro -o protein_in_membrane.gro > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.