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I would like to simulate the interactions between metal oxides surfaces (TiO2) and a biomolecule, I used AmbersTools (antechamber,parmchk2,leaf) to have the different parameters of my molecule and I have now two files prmtop (topology) and inpcrd (coordinate)

The aim is to simulate a system with enough molecule to have statistically representative data of different configuration of the interactions

But looking at Amber or NAMD manual, I don't see any parameters controlling the numbers of molecules, and moreover manual don't speak about static procedure but only dynamics which I don't want now.

Any help ?

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  • $\begingroup$ Why do you want to have many molecules on the surface rather than a single molecule in many different configurations? Do you have a suspicion that molecule-molecule interactions are important? Cause I imagine it will be quite a bit a bit more expensive to have multiple molecules present and choosing their orientations could be tricky. $\endgroup$ – jheindel May 2 '19 at 5:30
  • $\begingroup$ One molecule can be enough, but I will need to do multiple simulations with different configuration still, I need to have a .pdb with both the surface and molecule or I can have different pdb ? $\endgroup$ – Oka May 2 '19 at 10:41
  • $\begingroup$ It is hard to do MD even remotely correct if you have no idea about the basic concepts and try to learn everything from manuals. Also, I would suspect you don’t got anything meaningful on this system without explicit water molecules and reactive forcefields as water dissociates on many on the TiO2 surfaces. $\endgroup$ – Greg Jul 21 '19 at 15:34

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