# All Questions

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28 views

### Is there some free software to do some computation of Frank-Condon analysis?

I know Gaussian 16 can do it, but are there some free software to do? For simple excited state calculations using TD-DFT, we can use NWChem and Octopus.
307 views

### Are dispersion correction methods for DFT (such as D3) useful for geometry optimization?

For what I know the DFT-D3 method or similar corrections that take into account dispersion effect, add this type of contribution through calculation of atom pairwise interactions at the end of an ...
32 views

### LAMMPS data files, making atom IDs contiguous

I sometimes need to remove atoms from LAMMPS datafiles by hand, removing each row that corresponds to an atomID I want to remove, then decrementing the total atom count. This causes the atom IDs to no ...
484 views

### Which DFT functional should I use to simulate spectra of pesticides?

I am mainly searching for functionals to calculate spectra of pesticides. I found the benchmark test from Goerigk and Grimme$^1$, but don't understand which of the functionals suits my purpose the ...
98 views

### Why is there a large discrepancy between calculated frequency dependent dielectric function and experimental measurement?

I am calculating the frequency dependent dielectric function of $\ce{SiC}$ using VASP. After a geometry optimization, the INCAR file below is used for the ...
17 views

### Construction of dimeric protein models, selection and refinement

I want to perform a molecular docking between a protein of interest and several ligands. This membrane protein has a transmembrane domain composed of an alpha helix structure, which exerts it's ...
513 views

### What are good tools for visualizing glide planes and screw axes?

While there are a few tools for visualizing crystal structures, I'm particularly curious to know tools for visualizing space group symmetry, including: screw axes glide planes I teach a class on ...
33 views

### How to do a Sampling on the boundary of Brillouin zone in VASP

I use VASP to do my DFT calculation. I have to do a self consistent calculation to generate my CHGCAR. I want to ask is there anyway to write the KPOINTS file to generate K-meshing grid which can ...
25 views

### Ligand-protein molecular docking with different protonation states

It is known that protonation states of the receptor and the ligand before and after the binding are a very important factor for the binding, as indicated by both experimental data and computational ...
25 views

### Protein structure prediction

I want to perform a molecular docking between several ligands and the transmembrane domain of a protein. For this protein I only have the amino acid sequence, so it's necessary to do two things: ...
81 views