Department of Physics @ Carnegie Mellon

Theoretical and Computational Biological Physics

 

Part of the Biological Physics Initiative
Carnegie Mellon University, Department of Physics

www.cmu.edu
 
  budding simulation  

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!

 

 

 

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

 

ESPResSo

generic simulation package, especially suited for situations in which the user needs to supply non-standard routines, potentials, analysis, etc.

Gromacs

one of the standard atomistic simulation packages

NAMD

another one of the standard atomistic simulation packages

 

 

Visualization

 

VMD

well known tool to visualize data from atomistic or coarse-grained simulations

 

 

Packages

 

mbtools

PLUM

 

 

Scripts

 

gnu2eps

block

 
 
 

 
 
 
 

 

 

 

 
 
 
 
 
 
 

Scherk's minimal surface

Looking for a postdoc, PhD position or under-graduate research project or similar? Have a look at our announcements!

twisted torus

Funding:

NIH

NSF

 

Volkswagenstiftung