I built a force field for a complex. How can I check if the force field is working well or no?
I did a short molecular dynamics using AMBER only for the complex using the parameters I built. It worked well, but what can I do more ?
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asked Apr 16, 2022 at 14:18
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1$\begingroup$ How did you build the force field? I think usually the force field is checked against experimental data like radial distribution functions, equilibrium constants, ligand exchange rates etc. $\endgroup$– S R MaitiApr 16, 2022 at 19:35
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$\begingroup$ I have a complex that contain transitional metal, I want to do MD later, therefore, I build force field and parameter. There is no experimental data. I want to see if this force field works well for the complex or no? $\endgroup$– Abd-Elazeem MohamedApr 16, 2022 at 20:57
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$\begingroup$ I don't know how you can validate parameters if there are no experimental data. Do you have QM data? as in from high-level QM calculations. $\endgroup$– S R MaitiApr 17, 2022 at 9:29
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$\begingroup$ I have QM data. $\endgroup$– Abd-Elazeem MohamedApr 17, 2022 at 10:43
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1$\begingroup$ compare forces and energies against quality QM results. geometry optimize both MM and QM structures, calculate the RMSD for atomic positions. $\endgroup$– B. KellyApr 26, 2022 at 16:29
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1 Answer
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I tested the force field in two ways.
1-I performed a short-time MD for my system in vacuum using my force field and the same time of AIMD simulation for my system. Then I started to compare the evolution of the distance, the angle, and the dihedral between MD and AIMD. For example, Ru-N, N1-Ru-N2 etc.
2-Following the first step, I attempted to add more to compare by calculating the spectrum. As a result, I took 50 structures from the MD and AIMD simulations, ran the calculation, and plotted the spectrum for both (MD and AIMD).
answered Oct 27, 2022 at 9:05