[gmx-users] RE: Insertion of protein in lipid bilayer

[Graham Smith]

Dear Rob,

Assuming you have the conventional set up with the bilayer lying in the
x-y plane, try applying a position restraint in z only to the lipid (to
its P atom, for example). That might help keep the leaflets together,
while still allowing the lipids to move in the plane of the bilayer. I
think there's something about this in the html how-to file.

Graham

I have just seen that there have been a couple of messages about this in
the last few months - sorry for not replying before! You obviously
managed to solve the problem with binio.h. If Alok Jain hasn't given up
yet: it looks like you were using gmx version 3.2.1, whereas the
hole-making code was developed with 3.1.4 - that's probably the cause of
your compilation problems.

-----Original Message-----


Message: 4
Date: Thu, 28 Jul 2005 10:44:30 -0500
From: "rob yang" <nextgame at hotmail.com>
Subject: RE: [gmx-users] Insertion of protein in lipid bilayer
To: gmx-users at gromacs.org
Message-ID: <BAY104-F11C7F3D2C1157081BD321C6CF0 at phx.gbl>
Content-Type: text/plain; format=flowed

Hello gmx'ers,
I've been struggling with setting up md simulations of glycophorin A in
POPC

environment. I downloaded the make_hole program by Graham Smith and
followed

the tutorial as best as I could. My 2 layers of membranes fell apart
(from

looking at the trp file) and after about 130ps I got the following
error:

-----
Grid: 17 x 16 x 19 cells
WARNING: your box is exploding! (ncells = 5168)
atomic surface: building atom-vertex nn list...
----

So obviously there's some kinda user errors here as I used arbitrary

parameters and what not.
So if

anybody has done simulations using the make_hole program and wouldn't
mind

posting sample parameter files (.top, .mdp, etc) or sample system with

results (bible for us newbies), I would really appreciate it.

Thank you very much in advance.

Rob

############################################

Dr Graham R. Smith
Biosystems Informatics Institute
2nd Floor, Bioscience Centre
International Centre for Life
Times Square
Newcastle upon Tyne
NE1 4EP

Phone: +44 (0)191 211 2606
Mobile: +44 (0)7812 455 010
Fax: +44 (0)191 211 2598
e-mail: graham.smith at biiuk.com
http://www.biiuk.com

############################################







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