Dear Sir, thanks for the reply. what is the solution for this problem? can I just increase the box size? if so how? how to change the size without affecting the pope bilayer?
regards, pavithra Message: 4 > Date: Tue, 2 Jul 2013 12:10:37 -0400 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] problem in g_membed > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <CADUqwc5X4mFipUQO+aizXMv_JSmFD1bexwuyamk= > m+j+uhm...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Tue, Jul 2, 2013 at 11:36 AM, Pavithra <meetpavithra...@gmail.com> > wrote: > > > Dear gromacs users, > > > > I'm new to simulation. > > I'm running a membrane protein simulation with gromacs and am following > > KALP tutorial. > > I skipped inflategro and used g_membed command to insert my protein > complex > > into POPE membrane. > > I followed the tutorial and got the work done but with a peculiar error. > > few amino acid's atoms were protruding above the box were sliced and been > > added to the other side of the box.. > > is this possible?. > > > > Not only is it possible, it is expected. What you've described is the fact > that your box is of insufficient size to accommodate your protein. As a > consequence, PBC re-wraps the image of the protein such that it is within > the unit cell (since there is no such thing as "inside" or "outside" an > infinite system. > > > > since its the first time I don't know want information I have to provide. > > Please let me know if I have to send the mdp file or the command i've > used. > > > > When reporting problems, in general, such information is absolutely > necessary. In this case, probably not. > > -Justin > > -- > > ========================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Associate > > 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 > > > ========================================== > > > - > -- regards, Pavithra.K.B. -- 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
