What is the difference between fermi energy from DOS and Bandgap from HOMO-LUMO?

Hi. What is the difference between fermi energy from DOS and Bandgap from HOMO-LUMO? Should they both be same? relatively in my work the fermi energy calculated from DOS is double the bandgap...

06 July 2019 6,065 6 View

Is it possible to have LiC5 combination in case of Li ion adsorption on cathode material?

Hi. I am calculation adsorption Li ion on carbon surface. I find Li ion is adsorbed effectively on the surface forming LiC5. Also on modifying the carbon atom assembly by doping N and H, the...

04 May 2019 7,495 2 View

How to roll a 2-D sheet to 1-D tube?

Dear all I am working with 2-D sheets similar to that of graphene and BN sheet. I want to roll this sheet to 1-D tubes. Unlike graphene, they do not roll to sheets on optimization. Is there any...

31 December 2018 1,110 0 View

How to differentiate red and blue shift from UV spectrum obtained using computaion?

I have performed TDDFT for Heme molecule with imidazole axial ligand and obtained the absorption spectrum. Later I have added few gas molecules to Heme and the absorption spectrum is compared with...

31 December 2018 4,148 3 View

What charge and multiplicity should be used for Heme-Oxygen complex while optimizing using gaussian?

I want to optimise heme with oxygen molecule using gauissian. The Heme B structure with imidazole as one axial ligand and oxygen as another is used here. What should be the spin state of Fe here...

10 November 2018 1,096 0 View

What are the allowed electronic transitions that can be calculated from NBO analysis?

08 September 2018 8,019 4 View

What are the allowed electronic transitions that can be calculated from NBO analysis?

08 September 2018 9,688 3 View

What are the bonded parameters of fluorine molecule in OPLSAA ff for gromacs?

I want to add the bonded parameters for fluorine molecule in oplsaa ff. I find a term kb in the ffbonded.itp. How to obtain that value for F-F molecule?

06 July 2018 9,600 2 View

What will be the charmm script for SMD simulation of a dimer?

Hi. I wan to perform a steered MD simulation on a protein dimer. I would like to get some assistance in framing the charmm script for the pull code. The system consists of a dimer protein (Chain...

05 June 2018 4,001 3 View

How to analyse a Cluster.xpm file generated using Gromacs?

Hi I have simulated a protein for 100ns and the cluster analysis is performed. The xpm file is converted to eps. How should I read a cluster output and what does it infer. I have performed...

04 May 2018 8,139 6 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

What is the production process of CaFe ferroalloys?

I looking for ferro calcium production process

03 March 2021 1,755 4 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

Can water be extracted from Olivine?

I have always been interested in geology and wondered about how unique structures of materials behave in different circumstances. I stumbled upon Olivine, the magnesium iron silicate, and heard...

28 February 2021 7,330 4 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

How does charge on working electrode changes with rising potential?

During performing CV of a GCE or modified GCE, we rise the potential in the first half of the cycle and reduce it in reverse half. During the first half, what is the nature of charge on GCE or...

25 February 2021 7,994 3 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