Questions about establishing the Martini3 force field top file for thiophene ring structures. #44
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@zhangtrzhangtr Sorry for the late reply. Background on the choice of this constructions (which dates back to this paper and this PhD thesis) are explained in quite some detail in the M3 small molecule paper. It is what I called "divide and conquer" strategy. In brief, it is a convenient construction for a number of reasons, but mainly for the dihedral definition (it will be numerically stable given the ~90 degree internal angles) and relative simplicity. However, it's not a must. If you find that something else works better for your model, you should go with that. Please have a look at the "divide and conquer" strategy in the M3 small molecule paper and feel free to follow up. |
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@zhangtrzhangtr Sorry for the late reply. Background on the choice of this constructions (which dates back to this paper and this PhD thesis) are explained in quite some detail in the M3 small molecule paper. It is what I called "divide and conquer" strategy.
In brief, it is a convenient construction for a number of reasons, but mainly for the dihedral definition (it will be numerically stable given the ~90 degree internal angles) and relative simplicity. However, it's not a must. If you find that something else works better for your model, you should go with that.
Please have a look at the "divide and conquer" strategy in the M3 small molecule paper and feel free to follow up.