Calculate Radial Distribution Function using ONIOM gaussian results

07 July 2017 0 1K Report

Dear all,

I would like to ask to you all that I am performing the ONIOM calculation and want to calculate radial distribution function. So, Please let me, can I calculate radial distribution function using ONIOM results.

Badges
Science topic

More Nandan Kumar's questions See All

Missing pulling information while performing Steered Molecular Dynamics ?

Dear all, This is regarding the Steered Molecular Dynamics. After finishing SMD, extracted useful frames from the SMD trajectory and performed the brief NPT equilibration of the selected useful...

11 December 2019 6,880 2 View

Is there any other way to calculate the surface area per lipid of 200 ns trajectory, other than using MEMPLUGIN of VMD?

Hi Everyone, I am calculating the surface area per lipid of 200 ns membrane trajectory using MEMPLUGIN of VMD and it seems to be calculating the same too slow. Therefore, I would like to ask Is...

05 June 2019 3,497 4 View

CCSD(T) calculation of Open shell singlet cation ?

I would like to calculate the energetics for open shell singlet Sc+ and Sc+(OH2) using CCSD(T) level. As if we consider default Gaussian procedure, it seems to be considered close shell singlet....

11 December 2018 9,008 0 View

How can one continue the MD simulation in Gromacs if simulation has terminated, but not completed?

I am running the MD simulations for 30 ns which is 15000000 nsteps using dt= 0.02 using GROMACS software but it has terminated (after 13000000 steps) before completion due to queue limits. I would...

05 June 2017 7,479 10 View

Can anyone suggest me what type of atoms of phospholipid headgroup have to select for lipid headgroups density analysis?

As we know that density analysis is one of the worthwhile analysis to validate the our bilayer membrane model. I am using the gmx density of gromacs software to calculate the lipids headgroup...

05 June 2017 2,057 1 View

How can I get torsion potential?

Basically, I want to calculate the torsion angle potential (Vn) for the force field parameter development. For that I performed the potential energy surface (PES) scan with rotating a bond by 360...

11 December 2016 6,610 13 View

How do we calculate -center x y z (Coordinates of geometrical center), when we orient the protein in bilayer membrane?

I need to construct a mixed lipid bilayer for simulating a membrane protein. I am trying in GROMACS, but I have a problem in orientation of protein in lipid mixed type lipid bilayer.

05 June 2015 3,731 4 View

How can I prepare virus for a TEM or SEM imaging?

I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?

11 August 2024 3,115 1 View

Handling Missing Data and Building a Predictive Model with Incomplete Information ?

I am developing a predictive model for a water supply network that involves 20 influencing points. However, I only have historical data for 10 out of these 20 points. I would like to know how to...

10 August 2024 4,005 2 View

Is it possible to use the Fused Deposition Modeling (FDM) to additively manufacture interconnected porous structure generation of >100-200 micrometer?

Usually, additive manufacturing techniques like SEBM, SLS, and SLM are used for interconnected porous lattice structure generation with sizes of >100–200 micrometers. Can the Fused Deposition...

09 August 2024 7,892 0 View

How to define an anisotropic material with asymmetric elastic compliance/stiffness matrix in ANSYS APDL?

I need to model an anisotropic material in which the Poisson's ratio ν_12 ≠ ν_21 and so on. Therefore, the elastic compliance matrix wouldn't be a symmetric one. In ANSYS APDL, for TB,ANEL...

09 August 2024 5,048 2 View

How to calculate CCS for Sodiated adduct ions and Multiply Charged Ions?

I'm currently working on calculating the collision cross section (CCS) for various ions, and I'm facing challenges when dealing with sodiated and multiply charged ions. Most of the resources I’ve...

08 August 2024 8,329 0 View

How can I apply boundary conditions in an orthotropic steel deck numerical model using ABAQUS software?

I am trying to simulate vehicular loading on an orthotopic steel deck bridge section in ABAQUS software. The red arrow mark in the attached figure indicates the direction in which the vehicle will...

08 August 2024 719 0 View

Is changing the medium during the experiment overestimate the results?

I am experimenting with cancer and non-cancer cells in a 12-well plate for 4 days with a seeding density 1*10^4/well, however, I noticed that the control group growth rate slows down on D3. Should...

07 August 2024 2,283 2 View

Is it possible to plot the atom-projected band structure using GPAW?

Hi, I'm currently working on a project where I need to plot the atom-projected band structure using GPAW. I've been able to calculate the band structure for my material, but I'm having trouble...

07 August 2024 269 3 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

Can you suggest reliable sources defining "3D mesh" and "3D city models"?

Dear fellow researchers, I am currently working on a paper where I need to provide a reliable reference that defines and distinguishes between 3D mesh models and 3D city models. Although I am...

06 August 2024 9,986 2 View