New answers tagged molecular-dynamics
5
"But they cannot handle "exotic" materials. Why?"
You have claimed this without a reference! MD in principle can be done for any group of interacting particles, especially if you have an accurate forcefield. The issue is that classical MD with a classical forcefield will probably not do as well for an exotic material like a ...
23
Many published papers, even extremely highly cited ones by what you call "serious" authors, have issues like these.
Consider for example this one which currently has 862 Google Scholar citations, and has been used as a benchmark for the quantum dynamics of the seven density matrix diagonals in a 7-site model of the FMO complex. The authors were (...
14
I was actually going to provide this as a comment as this in itself is not a proper answer. But since this got a bit too lengthy for a comment, I am providing this as an answer.
It is possible for a highly cited paper to have non-equilibrated results. However, you should consider the fact that you may be using a different precision for your calculations. ...
7
You mentioned DFT, which is typically used to calculate the electronic energy at zero temperature. You can adjust the geometry until this electronic energy is lowest, but then you might ask why for a given pressure, if you increase the temperature, a substance's geometry changes, perhaps from an ordered lattice, to a disordered liquid, to a bunch of ...
8
"But since the DFT works not so well when dealing with semiconductors and excited-state calculations, wouldn't NAMD be too erroneous considering the nuclei vibrations?"
First of all, DFT in this context might not be as bad as you think. For example, my answer to: What are some recent developments in density functional theory? shows that even 10 ...
5
The current biomolecular force fields that I'm familiar with don't include any special energy terms for hydrogen bonds. Typically, hydrogen atoms that are capable of hydrogen bonding have very small Lennard-Jones radii and significant positive charges, which allow for very strong electrostatic interactions. For example, in the CHARMM force field, the alcohol ...
10
The short answer is that, while hydrogen bonds do have some covalent character, you can mimic that covalent character by increasing the electrostatic term. For example you can specify point charges to the oxygen and hydrogen atoms that are larger than they would otherwise be, and the overestimated electrostatic attraction will compensate for the neglect of ...
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