Bernd Ensing

Bernd Ensing

Hybrid MD with cm3d code

A pre-beta version of the cm3d molecular dynamics program including the adaptive atomistic/coarsegrained multiscale algorithm

Authors

Bernd Ensing

Here is a pre-beta version of the cm3d molecular dynamics program including the adaptive atomistic/coarsegrained multiscale algorithm. Feel free to have a look at the code. Currently the algorithm appears to work properly and stable and we are now at the stage to profile and tune the performance of the code. In particular the parallization needs to be fixed… Also there is currently not a good manual on how to setup your own system for a hybrid MD simulation with cm3d. There is actually a short manual that lists the keywords in LaTeX format provided with the source code. I guess that the source code is the best manual at the moment. In any case, you can consider yourself as being very brave to tryout this code at its current developing stage. Reports of bugs are always gratefully appreciated. Enjoy!

Program: cm3d.hybridMD.tar.gz
Save this file in a new directory and untar (tar -xzvf cm3d.hybridMD.tar.gz). Move to the “compile” directory and compile the source using/adapting one of the Makefiles, for example: “make -f Make.osx” on a Mac or “make -f Make.linux.fast” on a linux machine. A LaTeX manual is found in the directory “manual”.

Example run: hexane.tar.gz
Save this file in a new directory and untar (tar -xzvf hexane.tar.gz). Move into the created “hexane” directory and try to run the input using “cm3d.osx input > output” (assuming that the program was named “cm3d.osx” and is in the path). Note that with the provided input settings this simulation may take a couple of days on a fast computer.

References:

[1] Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics. Bernd Ensing, Steven O. Nielsen, Preston B. Moore, Michael L. Klein, and Michele Parrinello, J. Chem. Theory Comput. 3 (2007), 1100 – 1105, DOI: 10.1021/ct600323n

[2] Adaptive multiscale molecular dynamics of macromolecular fluids. Steven O. Nielsen, Preston B. Moore, and Bernd Ensing, Phys. Rev. Lett. 105 (2010), 237802 DOI: 10.1103/PhysRevLett.105.237802

Recent progress in multiscale molecular dynamics simulation of soft matter. Steven O. Nielsen, Rosa E. Bulo, Preston B. Moore, Bernd Ensing, Phys. Chem. Chem. Phys.12 (2010), 12401 – 12412 DOI: 10.1039/c004111d

Hybrid MD with cm3d code