Theoretical and Computational Biological Physics
Part of the Biological Physics Initiative
Carnegie Mellon University, Department of Physics
Resources
This site collects a number of useful resources that are part of the day-to-day research in the Deserno group. Feel free to use them, but please respect any terms and conditions that may apply to them. Some of these resources have been developed in the Deserno group, but not all of them. This page is under construction!
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mbtools tutorial |
If you want to learn how to use the membrane package mbtools and in particular get more familiar with the Cooke model for coarse grained lipid simulations, this is a good way to start. Download the tutorial as well as a tarball of scripts and see, whether you can get them to run! This tutorial was the practical part of the ESPResSo and mbtools section in several international workshops (one in Levi, one at CECAM in Stuttgart, and one at CECAM in Lausanne). The practical session was supplemented in the morning by an introductory talk on strongly coarse grained membrane simulations. You can download a pdf of this talk here (filesize: about 23MB). |
MD Simulation codes |
ESPResSogeneric simulation package, especially suited for situations in which the user needs to supply non-standard routines, potentials, analysis, etc. |
Gromacsone of the standard atomistic simulation packages |
NAMDanother one of the standard atomistic simulation packages |
Visualization |
VMDwell known tool to visualize data from atomistic or coarse-grained simulations |
Packages |
mbtools |
PLUM |
Scripts |
gnu2eps |
block |
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