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msmbuilder
MSMBuilder 1.0.1
Feb 12, 2011

Update to v1.0 that fixes scipy and gromacs compatibility issues. This release should work with any current release of scipy (presently up to v0.9) without giving strange implied timescales. It should also work with all the 4.x releases of gromacs. We highly recommend using the Virtual Machine with gromacs and MSMBuilder pre-installed for ease of use.Notes

Download Links

Feb 15, 2011
0
Any
Application/binary
VirtualBox virtual machine with MSMBuilder pre-installed

Feb 15, 2011
44 KB
Any
Application/binary
Instructions for installing MSMBuilder VM

Feb 15, 2011
6 MB
Any
Source code
Source code

Feb 15, 2011
29 MB
Linux
Application/binary
32-bit pre-compiled code for linux

Feb 15, 2011
9 MB
Mac OS X
Application/binary
Pre-compiled code for Mac OS X

Feb 15, 2011
1 MB
Any
Data/images/video
Instructions for tutorials

Feb 15, 2011
148 MB
Any
Data/images/video
Files for MSMBuilder tutorial

Feb 15, 2011
0
Any
Data/images/video
Materials (slides, videos, etc) for the workshop held in June, 2009

Documentation Links

Feb 15, 2011
Instructions for installing the precompiled code

Feb 15, 2011
User manual

PLEASE CITE THESE PAPERS

Bowman GR, Huang X, and Pande VS. Using generalized ensemble simulations and Markov state models to identify conformational states. Methods (2009)


MSMBuilder2
MSMBuilder2 is a complete overhaul of MSMBuilder. It features improved clustering algorithms and improved estimators for transition matrices. MSMBuilder2 works in Linux and OSX platforms. See Docs/Tutorial.pdf for complete installation instructions.
2.7.0
Jan 28, 2014

Download Links

Jan 28, 2014
50 MB
Any
Source code

PLEASE CITE THESE PAPERS

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. JCTC 2011. (2011)

Previous Releases


MSMBuilder 2.6.0

Mar 26, 2013

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Mar 26, 2013
46 MB
Any
Source code


MSMBuilder 2.5.1

Jul 28, 2012

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Jul 28, 2012
14 MB
Linux
Source code


MSMBuilder 2.5 beta

May 15, 2012

MSMBuilder2.5 (beta) includes performance enhancements, support for arbitrary distance metrics, hierarchical clustering, and improved PCCA+ lumping.Notes

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May 15, 2012
14 MB
Any
Source code


MSMBuilder 2.0.4

Jan 10, 2012

Minor improvements in PCCA, PCCA+

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Jan 10, 2012
12 MB
Linux
Source code


MSMBuilder2.0.3

Oct 22, 2011

Source code and installation files. Notes

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Oct 22, 2011
11 MB
Any
Source code


MSMBuilder2.0.2

Sep 19, 2011

Minor Bugfixes

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Sep 19, 2011
11 MB
Any
Source code


MSMBuilder2.0.1

Sep 02, 2011

Bugfixes for MSMBuilder2Notes

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Sep 02, 2011
11 MB
Linux
Source code


MSMBuilder2.0.0

Aug 23, 2011

Notes

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Aug 24, 2011
117 MB
Linux
Source code
Source code and example files. Based on SVN Revision 552


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