[gmx-users] Re: gmx-users problem in g_membed Digest, Vol 111, Issue 8

[Pavithra]

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 <jalemkul at vt.edu>
> Subject: Re: [gmx-users] problem in g_membed
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>         <CADUqwc5X4mFipUQO+aizXMv_JSmFD1bexwuyamk=
> m+j+UhmDZw at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> On Tue, Jul 2, 2013 at 11:36 AM, Pavithra <meetpavithramsc at 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
> ==========================================
>
>
> -
>



-- 
regards,
Pavithra.K.B.