How to produce potential energy trajectory for use in estimate_multi_temperature()

[hjuinj]

I am looking at the pyEmma tutorial using on Analyzing multi-temperature simulations with PyEMMA,

In order to use pyemma.thermo.estimate_multi_temperature, I need to input energy_trajs containing the potential energy at each time step. How do I produce this data at the first place, say if I have individual trajectories generated from GROMACS?

[franknoe]

In Gromacs I believe the tool to compute energies from trajectories and setups is called g_ener. In any case, this is not a PyEMMA issue. Please see Gromacs documentation.

Am 27/04/17 um 20:55 schrieb hjuinj:

I am looking at the pyEmma tutorial using on Analyzing multi-temperature simulations with PyEMMA http://www.emma-project.org/latest/generated/PyEMMA.thermo.estimate_multi_temperatur_-_asymmetric_double_well.html,

In order to use |pyemma.thermo.estimate_multi_temperature|, I need to input energy_trajs containing the potential energy at each time step. How do I produce this data at the first place, say if I have individual trajectories generated from GROMACS?

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Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354 Web: research.franknoe.de Mail: Arnimallee 6, 14195 Berlin, Germany

[hjuinj]

Ah thank you and sorry about that. I thought pyEmma has some tools to do that too.

[franknoe]

For umbrella sampling, yes, because it's easy to compute the umbrella bias energy if you are using a harmonic biases. But for temperature replica-exchange and other more complex forms of bias you need to be able to compute the energy of the molecular system, and that's the job of MD packages, because it depends on a variety of properties of your MD setup. PyEMMA can be used for the post-processing then.

Am 27/04/17 um 21:01 schrieb hjuinj:

Ah thank you and sorry about that. I thought pyEmma has some tools to do that too.

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Prof. Dr. Frank Noe Head of Computational Molecular Biology group Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354 Web: research.franknoe.de Mail: Arnimallee 6, 14195 Berlin, Germany