Matrix is singular
Posted: Fri Mar 22, 2013 8:22 am
Dear users and developers,
I'm trying to run EMMA for a ligand-protein binding event (for a very small organic molecule) for which I have several trajectories of 20ns each. After clustering, assigning snapshots to clusters and estimating the lagtime, if I estimate the transition matrix using -reversible as argument, all runs fine but if I do the same with out -reversible estimation the program mm_estimate yields the following error:
How can this happen to obtain a singular transition matrix? Is it due to insufficient sampling?
When should one use the -reversible argument?
Thanks for the help!
Daniel
I'm trying to run EMMA for a ligand-protein binding event (for a very small organic molecule) for which I have several trajectories of 20ns each. After clustering, assigning snapshots to clusters and estimating the lagtime, if I estimate the transition matrix using -reversible as argument, all runs fine but if I do the same with out -reversible estimation the program mm_estimate yields the following error:
Code: Select all
Exception in thread "main" java.lang.IllegalArgumentException: Matrix is singular.
at cern.colt.matrix.linalg.LUDecompositionQuick.solve(Unknown Source)
at cern.colt.matrix.linalg.LUDecomposition.solve(Unknown Source)
at cern.colt.matrix.linalg.Algebra.solve(Unknown Source)
at cern.colt.matrix.linalg.Algebra.inverse(Unknown Source)
at sherlock.emma.Pcca_Simplex.perform(Pcca_Simplex.java:205)
at sherlock.emma.cmd.PccaCmd.run(PccaCmd.java:177)
at de.martin_senne.jcommandline.AbstractCmd.check(AbstractCmd.java:33)
at de.martin_senne.jcommandline.AbstractCmd.go(AbstractCmd.java:45)
at sherlock.emma.cmd.PccaCmd.main(PccaCmd.java:282)
When should one use the -reversible argument?
Thanks for the help!
Daniel