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

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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 6,482 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 7,832 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 1,426 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 4,508 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 1,437 0 View

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

Hi all, From NBO analysis, I observe various electronic transitions that take place between two atoms such as σ* - n*, n* - n* which contribute to the maximum stability, σ - n*. Are these...

08 September 2018 8,360 4 View

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

Hi all, From NBO analysis, I observe various electronic transitions that take place between two atoms such as σ* - n*, n* - n* which contribute to the maximum stability, σ - n*. Are these...

08 September 2018 10,002 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 7,558 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 4,321 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 8,553 6 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Should I include H atom into C3N5 when i am doing DFT modelling?

Hi all, my experimental XPS results shown that my C3N5 sample consists of N-H bond, hence in this case I should incorporate the N-H bond into my DFT modelling. However, I do notice several papers...

07 August 2024 8,414 2 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

28 July 2024 673 3 View

Wrong out put for gmx x2top?

Dear users, I would like to simulate a zeolite structure in gromacs. I got the .cif file from IZA expanded in one direction in Materials Studio and exported a .pdb file. However, when I want to...

24 July 2024 367 4 View

What is the principle/mechanism behind aging of carbon (graphite) containing refractory mix for isostatically pressed refractories?

The resin bonded carbon containing refractories are aged before use. How time of aging is determined? And mechanism behind aging.

23 July 2024 3,205 0 View

Why binding energy is in positive number after performing mmpbsa?

I performed mmpbsa of protein-protein complex simulation on gromacs. My binding free energy is +166781. This complex is stable when experimentally produced in wet lab. In index.ndx I grouped...

19 July 2024 4,120 5 View

Can Langmuir constant related to bonding energy (Kl) and Freundlich exponent (1/n) indicative of ads intensity show opposite trends with temperature?

The adsorbate is Arsenic and the adsorbent is a soil

18 July 2024 332 8 View

How to resolve ‘[ atomtypes ] Invalid order for directive atomtypes’ error in Gromacs?

I have been using Gromacs 2021.7. I wanted to simulate two small molecules in water. But, while generating the ions.tpr, I am getting the following error. The topol.top and .itp files for each...

17 July 2024 9,897 4 View

How to create parameter and coordinate files for ligand in amber when FATAL error (maybe due to duplicate bond specifications) happens?

Hello, I'm trying to create parameter and coordinate files for a drug (PRG-A01) found on the following page: http://www.probechem.com/products_PRG-A01.html I used the guide made by Michael...

17 July 2024 3,472 3 View