Thanks for correction. i appriciate it :) Chen Gong
From: Justin Lemkul Date: 2014-06-09 19:58 To: gmx-users Subject: Re: [gmx-users] Regarding membrane construction 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. -- 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.
