I am new to Chemical Engineering, Doing some research in my field which required me to learn a totally new subject of molecular dynamics simulation.
I need to create pdb file of different complex surfactants and polymers. I want to use Avogadro. However there is no detailed technical info in the manual available about the detail of structure available. For example, I want to know the accuracy of default Bond angle and length and charges computed by the software
If you optimize the geometry using one of the force fields (MMFF94, UFF, etc.) the accuracy will be that of the underlying method. Otherwise, it depends on the accuracy of your geometry (i.e., not very accurate).
Ok thank you for your help.
the molecules I am going to work doesnt have their pdb file in any database. So now can be sure about charges, bond angle and length which are very crucial in molecular dynamic simulation.
Generally if you’re running MD, the bond lengths and angles will change during dynamics.