How we can calculate energy momentum tensor for the electromagnetic field?

03 March 2018 0 2K Report

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How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

Do you think can be any gas and oil reservoirs in central of Iran?

I want to know more about gas and oil reservoirs in Iran.

14 July 2024 3,350 2 View

How to apply virtual site for a polymer?

Dear All, I have a PDB structure for a complex and large polymer. I need to perform MD simulations using the OPLS-AA force field. I obtained the force field parameters from LigParGen and created...

11 July 2024 5,109 0 View

Can I use different force field for protein and ligand?

Hello, Dear! Generally, I used CHARMM36 + cgenff force field for simulaiton. But,, due to certain parts of lignad, force field cannot be generated using Cgenff. Can I use different force field...

10 July 2024 9,513 3 View

I need help to write a good simulation of the solar system and its travel around the galaxy.Can you help me finish the code?

This is the code I have. I would need: An initial configuration (position and momentum), the orientation of the ecliptic with respect to the direction of travel by the sun, The orientation of the...

09 July 2024 6,063 2 View

What is the best method for modeling the transmission and reflection of an electromagnetic wave incident on a magnetic multilayer thin film?

Previously, I successfully modelled the transmission and reflection of electromagnetic waves incident on non-magnetic materials. Please refer to my publications for details: 1- A polynomial model...

05 July 2024 1,396 2 View

I found trouble to run MD of my peptide with PTM in different force field. In Charm-GUI, it cant recognize the engineering residue. What can I do now?

I am working on my PTM project. I have some peptide. I got the result of doing MD of those peptide without PTM in different force field like Charm-GUI, Amber, Gromacs. Now I have to do MD of those...

05 July 2024 9,346 0 View

How validate the dynamic molecualr simulation with experimental data?

I used forcite module of Material Studio software to simulate the dissolution of zinc production waste in deep eutectic solvent. UFF force field has been used for the optimization of molecules,...

02 July 2024 7,494 1 View

Why my mesh independent fastener as beam cartesian type not working in abaqus?

i have attached my model and i have used point based mesh independent fastener using attachment points and type of connector is basic cartesian but this is not working as i apply displacement on...

02 July 2024 6,293 0 View

I tried to do simulation using YASARA software for an optimized ligand after docking but an error is coming what should I do?

The error message is "Angle parameter for atoms42-45-15 (cf-nu-ns) not found in the force field. Initialization is not possible, check atoms for incorrect bonds, then update the force field's...

27 June 2024 3,446 3 View