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I am currently busy with my master's research project and I'm trying to calculate the free energy of separation of two cellobiose molecules in ionic liquid, that is, calculate the free energy of separating two molecules from a distance of 35 nm to 215 nm. I have tried steered molecular dynamics with the Jarzynski relation, taking the logarithm of the radial distribution function and various umbrella sampling methods, but none of them seem to give me good FE profiles.

I think my system (1-butyl-3-methylimidaozlium acetate) just isn't going to give good FE profiles, but my supervisor is convinced that it will. I am currently trying thermodynamic cycles out so I hope that works.

So, my question is, what other methods for calculating the FE of separating the cellobiose molecules are there? And can you provide tutorials for me for those? I am aware of slow growth, ABMD, NFE, metadynamics, etc. but either these do not have any useful tutorials or don't work in the AMBER force field.

I have been struggling with this for more than two months now and my supervisor does not want me to stop my analysis. What other method can I use? Is there other computational methods available for determining the interaction between two systems?

Thank you in advance.

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    $\begingroup$ What does it mean to give 'good FE profiles'? What are you actually trying to investigate? What do you need that free energy profile for? Your system seems small enough to not rely on force fields, maybe something more sophisticated would work better, e.g. DFT with a solvent model. Are you starting from the contact ion-pair? What structures are you using? $\endgroup$ – Martin - マーチン♦ Jul 22 '18 at 18:54
  • $\begingroup$ I'm trying to simulate the dissolution of cellulose in ionic liquid. So, what my supervisor asked me to do is determine the free energy of separating two cellobiose molecules from each other in ionic liquid as to model the spontaneity of two cellulose strands dissolving and separating in my solvent. $\endgroup$ – LLCJ27 Jul 23 '18 at 5:30
  • $\begingroup$ My systems are cellobiose and 800 1-butyl-3-methylimidszolium acetate molecules. The whole project is based on using force fields, so I cannot use DFT, QM, etc. $\endgroup$ – LLCJ27 Jul 23 '18 at 5:31
  • $\begingroup$ Please edit your question to make it clearer what you are doing; your recent comments suggest something a lot different than what your question asks. $\endgroup$ – Martin - マーチン♦ Jul 23 '18 at 8:12

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