Re: [AMBER] Number of inter-conversions between minima on a FEL

From: Daniel Roe <>
Date: Wed, 3 Oct 2018 11:03:06 -0400


The 'calcstate' analysis command may do the kind of analysis you want.
This command lets you define different states based on specific
criteria, then calculates lifetimes and transitions. There have been
some recent improvements to 'calcstate' (see here: so I recommend using the
GitHub version of cpptraj. See the manual and the pull request for
more details.

Hope this helps, let me know if you have any issues.

On Wed, Oct 3, 2018 at 8:10 AM Chetna Tyagi <> wrote:
> Dear Amber users,
> How can we calculate the number of inter-conversions i.e. transitions
> between individual energy minima obtained on a free energy landscape of PCA.
> Is there a way to calculate that using cpptraj? I carried out dihedral PCA
> using cpptraj.
> I had it confused with the percentage of occurrence of each representative
> structure during the simulation.
> Any advice is appreciated..Thank you.
> --
> Best wishes
> Chetna
> _______________________________________________
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Received on Wed Oct 03 2018 - 08:30:02 PDT
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