plumed-code.org

cp2k.org

version_history [CP2K Open Source Molecular Dynamics ]

https://www.cp2k.org/version_history

Trunk (4.0, development). Here you can see which new features / functionality are available in the released versions of CP2K. Trunk (4.0, development). Features available or under development in the latest SVN version. Maximum Overlap Method (. Modified Atomic Orbitals (. Improvements on Toolchain and Development Tools (Prettifier). Libcp2k interface (C/C header). Remote Memory Access (. Various performance improvements and bug fixes. Pseudopotentials for the Lanthanide elements. Fast method for periodic.

srnas.sissa.it

Small RNAs in Silico | PLUMED 2.0 is out

http://www.srnas.sissa.it/home/plumed-2-0-is-out

ERC event at Città della Scienza. PLUMED 2.0 is out. October 4, 2013. Middot; Add Comment. A paper describing PLUMED 2.0 has been just accepted on Computer Physics Communications. The preprint is available for free on arXiv. More info on the PLUMED webpage. Tagged with →. Error 403: Your IP is being rate limited by Twitter. — @S RNA S.

srnas.sissa.it

Small RNAs in Silico | New technique to accelerate enhanced sampling simulations

http://www.srnas.sissa.it/home/new-technique-to-accelerate-enhanced-sampling-simulations

Our work presented at the 4th ZING conference on nucleic acids. Our work presented at Rice University. New technique to accelerate enhanced sampling simulations. December 12, 2014. Middot; Add Comment. The method is implemented in a separate branch. Of the PLUMED plugin. And will be merged before next release of this software. All the details can be found in a paper just accepted on J. Chem. Theory Comput. A preprint is available at arXiv:1412.3916. Tagged with →.

prg.washington.edu

Openings | PRG: Pfaendtner Research Group

http://prg.washington.edu/openings

PRG: Pfaendtner Research Group. Skip to primary content. Skip to secondary content. If you are interested in post-doctoral research opportunities in the Pfaendtner group please email the PI directly. Prospective graduate research associates should apply to the graduate program in the Department of Chemical Engineering. UW undergraduates seeking research experience should email Professor Pfaendtner directly with a statement of research interests. PRG wiki (login required). Other items of Interest.

prg.washington.edu

Publications | PRG: Pfaendtner Research Group

http://prg.washington.edu/publications

PRG: Pfaendtner Research Group. Skip to primary content. Skip to secondary content. 51 Hough, D. T. Schwartz, J. Pfaendtner, Detailed kinetic modeling of lignin pyrolysis for process optimization. 2016, Just Accepted Manuscript, DOI: 10.1021/acs.iecr.6b02092. 50 K G. Sprenger, Y. He., J. Pfaendtner. Probing How Defects in Self-assembled Monolayers Affect Peptide Adsorption with Molecular Simulation. 48 C Krumm, J. Pfaendtner, P. J. Dauenhauer. Chem Mater. 2016, 28 (9), 3108. 2016, 2 (4). 45 M A. Dono...

prg.washington.edu

Jim Pfaendtner | PRG: Pfaendtner Research Group

http://prg.washington.edu/jim-pfaendtner

PRG: Pfaendtner Research Group. Skip to primary content. Skip to secondary content. Jim Pfaendtner obtained his B.S. in Chemical Engineering (2001) from the Georgia Institute of Technology and his PhD in Chemical Engineering (2007) from Northwestern University under the supervision of Professor Linda J. Broadbelt. He subsequently was a research associate at the Center for Biophysical Modeling and Simulation (University of Utah, USA) under the supervision of Distinguished Professor Gregory A. Voth.

prg.washington.edu

Projects | PRG: Pfaendtner Research Group

http://prg.washington.edu/projects

PRG: Pfaendtner Research Group. Skip to primary content. Skip to secondary content. Representative Current Research Projects:. Interactions of Proteins with Interfaces and Solvents. Many novel materials show tremendous. Analysis of Complex Reacting Systems. Reaction networks are fundamental for understanding complicated chemical and biological processes. Researchers have provided many methods for using computers to generate reaction networks using computational and mathematical approaches. While ...

srnas.sissa.it

Small RNAs in Silico | Results

http://www.srnas.sissa.it/results

Our goals are twofold: (a) we develop new methodologies to improve molecular dynamics simulations and (b) we apply our techniques to relevant problems of RNA molecular biology. As such, also our results are twofold: Methods and Applications. A description of each of our publications can be found here. Alternatively, you can see all our papers indexed on Google Scholar. We dedicate a lot of effort to the improvement of PLUMED. And we recently collaborated to the development of its latest version. One of o...

vls3d.com

Vls3d - Simulation

http://www.vls3d.com/links/bioinformatics/simulation

Doctoral school for therapeutic Innovation. Computational Biology and Chemistry. Protein, DNA, RNA, Glycan modeling. Protein-protein docking, template-based docking. Hotspots, Interace residues, PPI modulators. PPI databases, network. Binding pockets and ligand-pocket datasets. Peptides, antibodies, epitopes. Visualization - commercial tools. Chemistry toolkits and utilities. Manage collections - chemical space. ADMET- physchem predictions - related tools. Off-targets, drug repurposing. An open source li...