During optimization of a matal-probe complex, the bonds among metal ion and donar atoms are vanished in the output file. Is it common?

I constructed an input file of metal ion bound probe. I added all the co-ordinate bonds as single bond and run the input file in Gaussian. But, in the output file, I got a structure where all the...

11 December 2017 2,035 4 View

I observed researchers are using different basis set to optimize and calculate HOMO-LUMO of organometallics. Which one is appropiate?

In top international Chemistry publications, I observed few are using LANL2DZ for both the metal and other atoms, few are using 6-311g type basis set for both the metal and other atoms and few are...

11 December 2017 5,016 4 View

How to calculate volume of a organic molecule in Gaussian?

I want to calculate the volume of a fluorescent probe and it's metal complex in Gaussian . What is the keyword to include in input file?

10 November 2017 7,268 5 View

What are the keywords in Gaussian 09 to calculate RDG coloured plot with VDW effect and 2D plot to calculate the non-covalent interactions?

I want to calculate RDG colour plot with VDW effect and 2D graphical plot to observe the non-covalent interactions like hydrogen bond, steric effect and van der Waalls forces in Multiwfn...

09 October 2017 5,129 3 View

How to include M06-2X in Gaussian 09 Revision A? It is not included in the theoretical model list. How to add this model?

06 July 2017 4,039 8 View

How would I calculate IRC of a bimolecular reaction using gaussian? I want to know the steps involved with sample input files?

I want to calculate the IRC of a bi-molecular reaction. The reactants are two beta-carboline type molecule and there occurs a proton transfer. Please inform the steps involved with sample input files.

11 December 2015 2,870 3 View

Which is the best basis set, theoretical model for hydrogen bond claculation using Gaussian?

I am working with a hydrogen bond receptor theoretically. Actually, I want to find IR, NMR, NBO charge, HOMO-LUMO energy gap, BSSE correction, PES scan, Theoretical fluorescence spectra using...

07 August 2015 4,045 17 View

How do I get the vertical excitation energy of a fluoride sensor in solutions theoretically using GAUSSIAN?

Actually I want to know the details method and sample input files. How the energy is calculated after getting the output file. I have already followed the SCRF keyword guideline given by GAUSSIAN....

07 August 2015 6,399 0 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

Does any one can help me choose a reasonable basis set for intermediate metal ions interactions with guanine (i.e Fe2+, Mn2+, Cu2+ and exc.)?

Hello every body Does any one has any idea to help me choose a reasonable basis set for intermediate metal ions (i.e Fe2+, Mn2+, Cu2+ and exc.) interactions with guanine or other DNA organic...

01 March 2021 6,187 2 View

How to formulate Energy minimization in Molecular dynamics simulation for alloys using meam potential?

during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...

22 February 2021 380 5 View

Magnetismic Gravity in the universe?

MAGNETISMIC GRAVITY What is magnetism? Something magnetic has a + and - charge. If 2 + or - are pushed if + and - are pulled. But what is the main reason for this? Why does magnetism have a pull...

21 February 2021 9,538 3 View

Has anyone succeeded in capturing uranium atoms in a fullerene structure?

Additional questions are: What are the encapsulating atoms? How difficult was the process and what rates were achieved? What factors most seriously affect the economics?

20 February 2021 3,134 5 View

How to get the vector of a specific vibration mode in phonon dispersion?

For example, I have this phonon dispersion(Fig. 1), and now I would like get vector of atoms which describes TA1 in P. I know v_sim can show vibrational animation of specific mode, but I do not...

20 February 2021 4,332 4 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View

How to combine two geometries in LAMMPS ?

I am trying to simulate contact angle of water on a quartz slab using LAMMPS. I have created and equilibriated the quartz slab and the water cluster separately. Now I want to create a composite...

17 February 2021 5,884 2 View

Rdf of atoms from a COM or point in lammps or VMD?

Hello all, as I understand there isn't any straight way to get an rdf of atoms from the center of mass or a coordinate of specific atoms in lammps. I wonder if anyone know any trick or way to get...

16 February 2021 2,517 2 View