December222012
Cut-away through a vesicle containing E.coli outer membrane proteins. This coarse-grained, solvated system is composed of over 1 million particles. It has been studied by MD simulations using the GROMACS simulation package on the IridisIII HPC resource at the University of Southampton

Cut-away through a vesicle containing E.coli outer membrane proteins. This coarse-grained, solvated system is composed of over 1 million particles. It has been studied by MD simulations using the GROMACS simulation package on the IridisIII HPC resource at the University of Southampton

vesicle GROMACS molecular dynamics simulation MARTINI coarse-grain iridisIII southampton computing HPC 

November132012
ssDNA in a simplified nanopore based on the alpha hemolysin barrel. Biophys J. 2012 Sep 5;103(5):1028-36. Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for sequencing; a Molecular Dynamics Simulation Study. Guy AT, Piggot TJ, Khalid S.

ssDNA in a simplified nanopore based on the alpha hemolysin barrel.

Biophys J. 2012 Sep 5;103(5):1028-36.
Single-Stranded DNA within Nanopores:
Conformational Dynamics and Implications for sequencing; a Molecular Dynamics Simulation Study.
Guy AT, Piggot TJ, Khalid S.

DNA nanopore biotechnology nanotechnology molecular dynamics simulation biophysical journal sequencing 

July112012

This movie shows the top view of a melittin (venom from honey bees) tetramer embedded in a POPE lipid bilayer. 

melittin simulation molecular dynamics peptide antimicrobial membrane lipids 

June102012

CECAM meeting on Free Energy Calculations

Free energy calculations: From theory to applications

June 4, 2012 to June 8, 2012

Location : Ecole des Ponts, Champs-sur-Marne, France.

http://www.cecam.org/workshop-695.html

This workshop featured talks from a combination of  established high profile speakers as well as younger researchers.

A number of themes arose from this workshop, the overarching one being that there is still no ‘best way’ to calculate free energies from molecular simulations. Workshops like this, are essential in facilitating discussion and disseminating the latest findings. Given  that new methods are being developed and refined, disseminating the latest progress in a timely fashion is of utmost importance. 

A very useful resource from Michael Shirts’ lab:

http://www.alchemistry.org/wiki/index.php?title=Main_Page

free energy simulation molecular dynamics monte carlo delta G 

May192012
FhuA; a TonB-dependent transporter from the outer membranes of E.coli. Rendered with VMD

FhuA; a TonB-dependent transporter from the outer membranes of E.coli.
Rendered with VMD

E.coli Gram-negative bacteria graphics membrane molecular dynamics outer membrane protein transporter vmd science render 3D illustration 

May152012

4-year industrially funded PhD studentship available!

Please contact Syma Khalid: S.Khalid@soton.ac.uk for further details

PhD studentship industrial graduate student molecular dynamics 

April282012

CCPBioSim workshop: How To Set Up a Protein Simulation

This free, one day workshop held in Cambridge was a successful first event for the EPSRC-funded CCPBioSim initiative. The 16 conference attendees had a busy day of learning theoretical aspects of running molecular dynamics simulations of soluble proteins, as well as hands-on practical work. The workshop was run by Dr Syma Khalid (Southampton) and Dr Peter Bond (Cambridge)

epsrc Khalid Bond Cambridge CCPBioSim molecular dynamics protein modeling 

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