I have been running a simulation on the formation of a drug-loaded polymeric micelle. The starting system is a packed box filled with polymers and drugs placed randomly. My colleague also ran an analagous simuation using the same mdp files.The optimized structure and thus partial charges of our drug atoms are slightly different, but it is chemically the same drug. We followed the same procedure for packing (using packmol), preparing the box, minimization, equilibration, and production. However, my colleague was able to obtain a nice spherical micelle, while my micelle has a more irregular shape. I’m wondering if getting an irregular micelle is a problem at all, and if so, what could have gone wrong?
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There are multiple reasons why this can happen:
- Starting with same input files can lead to different outputs/trajectories. Does your colleague ALWAYS get the spherical micelles or is it just from a single run? I have myself seen that running different simulations (3 independent runs) from same input files can produce micelles with different aggregation numbers.
- The partial charges, if significantly deviating, can lead to changes in micelle structure. Are the partial charges on the drug and the polymer same?
- If the box size or number of polymer chains change, the micelle morphology can change.
- What is the measure of “irregular micelle”? Is it just visual inspection or any quantitative measure? Polymer chains extending in the external phase (presumably water) can acquire a large number of different conformations which can give an impression of an irregular external morphology. See if the inner diameter is comparable.
- My colleague always gets spherical micelles with different concentrations of drug.
- The partial charges on the drug are different. The charges for the polymer are the same.
- We are using the same type of polymer and box size. In particular, 50 polymer molecules and 100 drug molecules.
- By visual inspection.
It is such a strange problem. Thanks!
I guess the problem then lies with the difference in partial charge on the drug.
If the model of the drug is different, the outcomes of your simulation will be different.
Thanks! Is there a way to tell which model is better than the other?
Whichever model produces the best agreement with target data and subsequent validation against known experimental properties is the one to use.