There is an option of using PLUMED along with MD simulation (via gromacs) to interpret the free energy of a given system. But, in case we want to directly access the free energy from energy output or any other output file of MD simulation (via gromacs), then how to proceed? Please advise. Thanks.
Free energies cannot be accessed by g_energy in general. You could use g_lie which uses the separated energy terms employing the LIE equation. But that's (as far as I know) a very inaccurate determination. You can use thermodynamic integration, umbrella sampling combined with weighted histogram analysis or probabilistic approaches using Metadynamics or replica exchange molecular dynamics. However, that is by far different from a conventional MD simulation.
Hello Sabahuddin,
Emanuel\s answer is as good as it can be given your question but still the results are not going to be even near approximate. The best option would be to use..one of the advance sampling techniques depending upon the size of your complex and computational facilities available at CDRI, Lucknow..or may be the sister CSIR labs in Lucknow.
Good Luck
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