Poster (Scientific congresses and symposiums)
Gaining speed in molecular dynamics simulations by implicit representation of water and membrane molecules
Steinhauer, Sven; Crowet, Jean-Marc; Brasseur, Robert et al.
2013Biomedica Life Science Summit
 

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Keywords :
Implicit membrane; force field
Abstract :
[en] Molecular dynamics (MD) is an appropriate method for investigation of peptide-membrane systems and helps in analyzing results from experiments. In many cases, the ability of viral fusion proteins and toxins for destabilizing the membrane is due to their hydrophobic profile, leading to particular membrane insertion. By now, many relevant processes for drug design, toxicological studies and other fields of application, are not feasible by MD simulations, when each atom is represented over time. Processes such as protein folding, often take place above the time scales reachable by MD simulations, which are of the order of micro seconds. The necessary time effort for carrying out such simulations stays considerable and depends mainly on (1) the complexity of the simulated system (2) the simulated time scale (3) the simulation method (4) the efficiency of used hardware and software algorithms. Nowadays, MD simulations can still take weeks of calculation on high end computers. Impala is an implicit water and lipids forcefield, initially developed by our laboratory. Implicit forcefields replace water and/or lipid molecules by a couple of simple and partially precalculable equations. Using this method, thousands of water and lipid molecules can be replaced in MD simulations using Gromacs software. This leads to a considerable reduction of system complexity. The original Impala algorithm based on the assumption of rigid peptides and used a Monte Carlo algorithm with the aim of finding the insertion characteristics of these molecules in membranes. Our current work is the integration of the Impala forcefield into Gromacs, a freely accessible MD software. Replacing the aqueous and lipid phase atomic description in Gromacs MD by an implicit forcefield is supposed to lead to a gain of speed compared to full atomistic simulations. A gain of precision compared to Impala is expected, too. This will be achieved by turning molecules flexible, when implementing Impala into Gromacs.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Steinhauer, Sven ;  Université de Liège - ULiège > Chimie et bio-industries > Biophysique moléc. numér.
Crowet, Jean-Marc ;  Université de Liège - ULiège > Chimie et bio-industries > Biophysique moléc. numér.
Brasseur, Robert ;  Université de Liège - ULiège > Chimie et bio-industries > Biophysique moléc. numér.
Lins, Laurence  ;  Université de Liège - ULiège > Chimie et bio-industries > Biophysique moléc. numér.
Language :
English
Title :
Gaining speed in molecular dynamics simulations by implicit representation of water and membrane molecules
Publication date :
19 June 2013
Number of pages :
A0
Event name :
Biomedica Life Science Summit
Event organizer :
TEMA Technologie Marketing AG, Viktoria Lhomme
Event place :
Aachen, Germany
Event date :
from 18-06-2013 to 19-06-2013
Audience :
International
Available on ORBi :
since 21 June 2013

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