[gmx-users] lipid simulations

[Syma Khalid]

Hi,

I thought Chris' reply was more than adequate. All the other information you
need you can get from papers by amongst others, the groups of: Tieleman,
Marrink and Sansom.

All that is needed is some background research and maybe a little (with the
info out there, it need only be very little) trial and error.

-Syma


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

Dr. Syma Khalid                    e-mail:  syma.khalid at bioch.ox.ac.uk
Dept. of Biochemistry              phone:   (0)1865-275380
University of Oxford               fax:     (0)1865-275273
South Parks Road                
Oxford
OX1 3QU
U.K.
________________________________

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Chris Neale
Sent: 18 August 2007 20:51
To: gmx-users at gromacs.org
Subject: [gmx-users] lipid simulations

>thanks for such a brief reply..

Considering that this is a volunteer mailing list, I don't consider my
response to be brief. 
I'm not sure what you were hoping for. I have given you some good leads and
a rather detailed 
outline of the details that are most difficult to pick out of the papers.

>i have already downloaded these four files from the Peter Tieleman's
>website:
>"dppc128.pdb  dppc.itp  inflategro.pl  lipid.itp"
>but it looks like it has been simulated in water box for some time..
>am i right? (i am afraid that i will not)

That information is available in the papers that are referenced on the
website from which you
downloaded those files. Every single downloadable file on that web page is
associated with a paper.
The reference numbers on that site are not correct but it shouldn't take you
more than an hour to figure out which references you need to read.

>then what's next...

I am not going to answer that one. 

>...and what will be the *.mdp file for this simulation.

I have given you the lipid-specific mdp options. If you don't understand how
to translate my
description into an mdp file then I suggest that you consult the gromacs
manual.


Chris.

>>/ what parameters should I use for lipid simulations
/>/
/>/ That depends on the forcefield that you are using. I will tell you
/>/ about what I do but this is a poor substitute for what you should
/>/ really be doing, which is:
/>/
/>/ 1) find the initial paper that publishes the forcefield that you are
/>/ using and figure out how they used it
/>/ 2) Find some very recent papers that use this same forcefield and
/>/ figure out how they use it and then read the relevant papers that they
/>/ reference in their methods section.
/>/
/>/ That said, I use the forcefield having a united atom representation of
/>/ lipids originally proposed by Egberts et. al. (1994), with the charges
/>/ from Chiu et. al. (1995), adjusted by Berger et. al. (1997), and with
/>/ the additional scaling of 1-4 coulombics introduced by Lindahl and
/>/ Edholm (2000). You can download these topologies from Peter Tieleman's
/>/ website:
/>/ http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
/>/
/>/ It is common to use a twin range cutoff with LJ calculated every step
/>/ up to 1.0nm and up to 1.4nm every 10 steps when the nonbonded list is
/>/ updated. Coulombics are in real space below 1.0nm and by PME beyond.
/>/ Pressure coupling is a semiisotropic berendsen barostat with tau_p of
/>/ 4.0ps. Temperature is coupled to a berendsen thermostat separately for
/>/ i)lipids ii)water+ions iii)protein witha tau_t of 0.1ps. I use lincs
/>/ to constrain all-bonds.
/>/
/>/ Note that I personally reduce the short range interaction cutoff to
/>/ 0.9nm from 1.0nm. But you would be better to stick with parameters
/>/ that are in more common usage.
/>/
/>/ The protein forcefield that I use is opls-aa and I use tip4p water.
/>/ When combining these forcefields, I use an unpublished method to scale
/>/ 1-4 coulombics differently for protein and lipid:
/>/ http://www.gromacs.org/pipermail/gmx-users/2006-September/023761.html
/>/ There are also a variety of related posts that come after that one but
/>/ I can't remember what they are. You are going to need to do some
/>/ searching.
/>/
/>>/ how to insert the protein in that bilayer.
/>/
/>/ You can either use the make_hole version of mdrun available for
/>/ download from the user contributions section of the gromacs web site
/>/ of a program called inflategtro available from Peter Tieleman's
/>/ website: http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis
/>

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