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 is the hybridization of Fe metal atom in heme with two axial ligands?

What is the hybridization of Fe metal atom in heme with two axial ligands? and what will be the hybridization with one axial ligand? How to calculate it? Thnak you

08 September 2018 7,194 3 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

How the parameters (such as Mw, Chemical bonds, polymer bland and so on) affect the mechanic property of polymer (such as storage, loss modulus) ?

Anyone can recommend any books on such topics? Thanks in advance.

02 March 2021 8,457 2 View

How can you bring two structures together to create an adhesive bond in LAMMPS?

I have created an Ice 1h crystalline structure and an Aluminium substrate structure and equilibrated both at 250K. Now I need to bring them together in a way that an adhesive bond is created....

01 March 2021 3,325 2 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

I am looking for a simple software program to model 3D chemical bonds. The purpose is to generate high-quality graphical abstracts. Any suggestion?

Hello everyone: I am looking for a simple software program to model chemical bonds. The purpose is to generate a high-quality graphical abstract for a top leading journal in the field of...

23 February 2021 8,012 3 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

How to interpret this FTIR spectrum of pyrolyzed hydrochar?

20 February 2021 2,840 3 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View