[gmx-users] Re: big membrane

[Kia Balali-Mood]

Hi Michael,

What ensemble are u running the sim with? is it NPT or NPAT?
My experience is that u could run an NVT ensemble first (NOT my idea but that
of a certain Dr Peter Tieleman!), then an NPT with
solvent it's likely to work with a zwitterionic system such as a DMPC bilayer.

Alternatively try this
EM the big membrane then do a short MD (NVT) (~20ps) with NO spc/solvent.

I presume ur pressure is 1 atm?

best of luck

Kia

>
> Message: 7
> Date: Tue, 9 Nov 2004 12:05:47 +0200
> From: Michael <mgang at pob.huji.ac.il>
> Subject: Re: [gmx-users] big membrane
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <ED356F1A-3236-11D9-AA1E-000A95BA144E at pob.huji.ac.il>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Dr. Warren
> Thank you for your kind response.
> I have now a new problem.
> After I make the bigger membrane with genconf and make energy
> minimization the system explodes.
> (The energy after the em is somethink like e-15)
> Have you an idea how to solve it?
> Thanks in Advance,
> Michael Gang.
>
> On Nov 8, 2004, at 2:04 AM, Dallas Warren wrote:
>
> > The biggest bilayer I've got is with a box of 6.176 6.176 6.608 and
> >  when i try to put the protein in the membrane it destroys the
> > membrane.
> >  Does anyone know where i can get a dmpc bilayer large enough to put
> > the
> >  protein in it ?
> >  If not,maybey has anyone an idea how to make the membrane bigger?
> >
> >  Why don't you use genconf and make it a 2x2x2 layer?  Or something
> > like that.
> >
> >  Catch ya,
> >
> >
> > Dr. Dallas Warren
> > Research Fellow
> > Department of Pharmaceutical Biology and Pharmacology
> >  Victorian College of Pharmacy, Monash University
> >  381 Royal Parade, Parkville VIC 3010
> > dallas.warren at vcp.monash.edu.au
> > +61 3 9903 9083
> > -----------------------------------------------------------------------
> > ---
> > When the only tool you own is a hammer, every problem begins to
> > resemble a nail.
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> -------------- next part --------------
>

******************************************************************************
Kia Balali-Mood
Laboratory of Membrane Biophysics
Division of Veterinary Biomedical Sciences
College of Medicine & Veterinary Medicine
The Vet School
University of Edinburgh
Summerhall
Edinburgh, EH9 1QH
Tel. +44 (0)131 650 6142
Fax. +44 (0)131 650 6576
leaflet.vet.ed.ac.uk