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EMMA
Command line tools and documentation of EMMA
Emma-1.4.1
Jul 02, 2013

Fixed: Reading interleaved trajectory does not advance to next trajectory.  

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Jul 02, 2013
5 MB
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Previous Releases


Emma-1.4

Jun 11, 2013

TRAM and ICA algorithm and command line tools added. Minor bug fixes.  

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Jun 11, 2013
5 MB
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Emma-1.3.1

Aug 10, 2012

*Bug fix, for clustering with stepwidth larger than 1 *Bug fix, clustering on disc for reg temporal and regspatial clustering  

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Aug 14, 2012
4 MB
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Emma-1.3

Apr 03, 2012

  

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Aug 02, 2012
4 MB
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Emma v1.2.5

Mar 06, 2012

Emma 1.2.5 (compared to 1.2.2) fixes: - an issue in ImpliedTimescales calculation (mm_timescale) which caused a NullPointerException under certain situations. - an issue in ImpliedTimescales calculation which caused only the first implied timescale to be correct. - a bug in mm_tpt, which results in output data consisting only of zeros.   

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Mar 06, 2012
1 MB
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Emma v1.2.5


Emma v1.2.2

Oct 14, 2011

Emma 1.2.2 (compared to 1.2.1) fixes a major bug concerning the restrictToStates option. New features of version 1.2.x include: - mm_observables to analyze MSMs and allow comparison with experimental measurements - detection of dynamical connected microstate - improved count matrix prior when estimating transition matrices - improved reversible transition matrix estimation  

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Oct 14, 2011
18 MB
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Emma v1.2.1

Sep 28, 2011

Emma 1.2.1 includes minor bug-fixes compared to version 1.2. Emma is now available in version 1.2. New features include: - mm_observables to analyze MSMs and allow comparison with experimental measurements - detection of dynamical connected microstate - improved count matrix prior when estimating transition matrices - improved reversible transition matrix estimation  

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Sep 28, 2011
18 MB
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Emma v1.2

Sep 02, 2011

Emma is now available in version 1.2. New features include: - mm_observables to analyze MSMs and allow comparison with experimental measurements - detection of dynamical connected microstate - improved count matrix prior when estimating transition matrices - improved reversible transition matrix estimation   

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Sep 02, 2011
18 MB
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Emma v1.2


Emma v1.1

Jan 21, 2011

Emma is now available in version 1.1. New features included: - algorithm for performing Transion Path Theory (TPT), which allows the analysis of the essential statistical features of reactive transitions - Perron-Cluster-Cluster Analysis (PCCA), a dynamical clustering method, which reveals metastable states  

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Jan 21, 2011
17 MB
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Emma v1.1 by 2011-01-21


Emma v1.0 patch by 2010-10-04

Oct 04, 2010

Patched version v1.0Notes  

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Oct 07, 2010
16 MB
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Emma v1.0 patched version by 2010-10-04


EMMA v1.0

May 31, 2010

  

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May 31, 2010
16 MB
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EMMA 1.0


GSGS-peptide data
Siulation data from a Gromacs simulation of MR121-GSGS-W - peptide. For more information refer to the documentation
GS_Peptide_data_1.0
Apr 03, 2012

  

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Apr 03, 2012
255 MB
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Tica Data
Two distance trajectories needed as input for the tica module of EMMA
Tica Data
Jun 13, 2013

Tica Data  View License

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Jun 13, 2013
99 MB
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