The output file contains all the information of the trajectory of the above problem, after MD simulation you get the results with x,y,z axis information.

Hello Rocco Caliandro,

Thanks for your response. I have sent you a mail concerning the tool. And in fact, I am interested in quantifying the 'flexibility' of a set of potential functions. I had employed different potentials to generate trajectories of the same peptide, and after performing geometric clustering I noticed a particular force field was more 'flexible': and of course, an impression of the relative 'flexibility' may readily be obtained from the number of clusters. And I will be glad if I can employ your tool to better describe and explain the observation.

You can get entropy from the FT transform of the velocity autocorrelation function for a short MD trajectory. Details here: https://www.researchgate.net/publication/231211130_Two-phase_thermodynamic_method_for_accurate_free_energies_for_liquids_directly_from_molecular_dynamics_simulations

Article Two-phase thermodynamic method for accurate free energies fo...

In our group (www.gnm.cl) here in Santiago, Sergio Davis has just written a paper on the topic, that allows you to estimate entropy directly from the MD. See "Calculation of microcanonical entropy differences from configurational averages",

S. Davis, Physical Review E 84, 050101(R) (2011). Now he has an improved method.

You can ask directly [email protected]

Normal mode calculations or quasi-harmonic analysis are two accepted methods. I haven't gone through the publication by Sergio Davis, read it. It might offer a better and easier way out.

Best,

/A