[gmx-users] Re: mixed bilayer

[Kia Balali-Mood]

Hi Robert,

My experience is that it's better to couple (both temperatrure and pressure)
the lipids separately, particularly as it sounds like you have a mixed
zwitterionic lipid and anionic lipid bilayer.

Try an NVT ensemble before the NPAT or NPAT ensemble. about 40ps should be
enough
for an NVT, though it depends how big your bilayer is!


Best of luck

Kia

> ------------------------------
>
> Message: 4
> Date: Tue, 7 Dec 2004 16:13:56 +0000
> From: Robert d'Rozario <ROZARIO at biop.ox.ac.uk>
> Subject: [gmx-users] (no subject)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <Pine.VMS.3.91-2
> 	(vms).1041207161349.52195C-100000 at fennel.biop.ox.ac.uk>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
>
>
> Hi
>
> I have a mixed bilayer and I want to run a simulation but I do not know
> whether
> to temperature couple the two different lipids together and make them one
> group
> or to leave them seperate.
>
> One of the lipids is neutral overall and the other has an overall charge
> of -1.
> I have added counter ions to make the whole system neutral.
>
> Any advice would be greatly appreciated.
>
> Kind Regards
>
>


******************************************************************************
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