[AMBER] MMGBSA: estimating "effective energy" convergence

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 02 Nov 2016 15:38:36 +0200

I’m dealing with a homodimer and have calculated the “effective energy” of binding of the two subunits using MMGBSA.

The calculation was done from as single trajectory MD simulation.

In order to check whether the “effective energy” of binding has converged, I would like to extract the time-series of the sums of gas-phase energies and solvation free energies as computed for the trajectory snapshots of the unbound subunitA, subunitB, and the complex subunitA – subunitB.

I guess, I can do this by parsing the temporary files obtained (e.g. _MMPBSA_complex_gb.mdout) that contain the energy components. My question is if there is a better way of doing what I described above.

Thanks in advance for any suggestions

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Received on Wed Nov 02 2016 - 07:00:03 PDT
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