
Made with VMD
Biological membranes are complex assemblies of diverse lipids,
and molecular dynamics (MD) simulation has been among the most
effective biophysical tools to investigate them at an atomic-detailed level.
Nevertheless, capturing the wide range of lipid compositions and
their mixing continues to pose a major challenge to simulations,
due to the very slow diffusion of lipids.
This issue is particularly important when membrane proteins are present
in the membrane and one is interested in studying how they interact with
lipids. One solution to partially address this problem is to randomize
the initial configuration of lipids in replicate simulations.
The Center has developed a toolkit to rapidly clone a membrane with a
specific lipid composition into as many copies (with shuffled lipids)
as needed within a matter of minutes.
The Membrane Mixer Plugin (MMP)
uses advanced features in
NAMD to remove
clashes and make room before shuffling the lipids;
it also performs several checks to test the quality of the generated membranes.
This method can be accessed via a user-friendly GUI interface in the latest
version of VMD.
The Future of Biomolecular Modeling
A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee.
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NAMD History: The Drama
In the 1980s Klaus Schulten let two students build him a supercomputer. This
risky project, and a 1990s student revolt, led to NAMD. Now with 50,000 users
worldwide, this article charts the colorful history of NAMD. By Lisa Pollack.
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Announcements
NAMD and VMD share in COVID-19 Gordon Bell Special PrizeUIUC establishes oneAPI academic Center of ExcellenceSARS-CoV2 Simulations on Microsoft AzureArgonne Honors Fellow for COVID-19 Research Effort
Seminars
Remembering Klaus Schulten
Recent Publications All Publications
- Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys., 153:044130. 2020.
- Structural basis for the reaction cycle of DASS dicarboxylate transporters. eLife, 9:e61350. 2020.
- Twisting and tilting of a mechanosensitive molecular probe detects order in membranes. Chem. Sci., 11:5637-49. 2020.
- A CLC-ec1 mutant reveals global conformational change and suggests a unifying mechanism for the Cl-/H+ transport cycle. eLife, 9:e53479. 2020.
- Computational Dissection of Membrane Transport at a Microscopic Level. Trends Biochem. Sci., 45:202-216. 2020.
- Microscopic Characterization of GRP1 PH Domain Interaction With Anionic Membranes. J. Comput. Chem., 41:489-499. 2020.
- Probing cholesterol binding and translocation in P-glycoprotein. Biochim. Biophys. Acta Biomembr., 1862:183090. 2020.
- Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayers. Proc. Natl. Acad. Sci., 117:1788-1798. 2020.
Highly Cited
Neural gas for vector quantization and its application to time-series prediction. IEEE Transactions on Neural Networks, 4:558-569, 1993.
Click here for other highly cited papers
Click here for other highly cited papers