Hi HM,
I used for membrane-protein systems (peptide in your case) Gromacs. There are several papers about similar issues like yours.
Lemkul, J.A. and Bevan, D.R. (2008) A Comparative Molecular Dynamics Analysis of the Amyloid β-Peptide in a Lipid Bilayer. Arch. Biochem. Biophys. 470 (1): 54-63.
Lemkul, J.A. and Bevan, D.R. (2009) Perturbation of membranes by the amyloid β-peptide - a molecular dynamics study. FEBS J. 276 (11): 3060-3075.
Lemkul, J.A. and Bevan, D.R. (2011) Characterization of Interactions between PilA from Pseudomonas aeruginosa Strain K and a Model Membrane. J. Phys. Chem. B 115 (24): 8004-8008.
Also, you should take a look of Justin Lemkul's website: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/research.html and trying to use (or merge) this tutorials:
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html
Best regards,
Aldo
=======================================
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: asegurac.ipn.mx; aldosegura.gmail.com
website: www.bioinfolab.org.mx
=========================================
________________________________
De: HM <scienceamber.gmail.com>
Para: AMBER Mailing List <amber.ambermd.org>
Enviado: Viernes, 18 de enero, 2013 3:07:11
Asunto: Re: [AMBER] Membrane-Peptide Simulation ( peptide going away from membrane)
Thank Ross,
I am new to Umbrella Sampling, It would be nice if I will get some help
from a nice tutorial. I searched but could not find a good one.
I have a query regarding the system complexity. Since I have limited
processors to run the job, shall I try Umbrella Sampling in implicit
solvent, will the results reliable?
Thanks,
On Fri, Jan 18, 2013 at 9:38 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> would take a good look in the literature at what people do in these
> situations. The issue with your 'control' is that you make no mention of
> timescale. The experimental data may indeed show that the peptide
> penetrates the membrane but does it give any indication of the timescale
> that this takes? If it is on the order of milliseconds then just running
> brute force MD is not going to work. One option would be to try some form
> of umbrella
>
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Received on Fri Jan 18 2013 - 05:30:03 PST
