Zeynab Mohammad Hosseini Naveh

6 Questions 10 Answers 0 Followers

Questions related from Zeynab Mohammad Hosseini Naveh

Does CHARMM-GUI Drude-Prepper input generator work for MD simulation of carbon nanotubes?

Dear all, I have the intention to perform molecular dynamics (MD) simulation of carbon nanotubes (CNT) using Drude polarizable force field implemented in NAMD. I‌nitially, I used CHARMM-GUI to...

25 July 2021 2,069 1 View

What is the best software to perform molecular dynamics simulation using polarizable force field?

Dear all, I'm in principle a NAMD user but I'm new in performing MD simulation using polarizable force field. I wonder if anyone can suggest any MD software (NAMD or GROMACS, or ..) to implement...

15 July 2021 1,828 2 View

Which parameters to use in the MD simulation of defected carbon nanotube/graphene?

Hi All, I want to perform Molecular Dynamics (MD) simulation (using NAMD and CHARMM force field) of carbon nanotube/graphene with topological defect like Stone-wales. Creating topological defects...

27 May 2018 5,778 3 View

How to calculate the heat of solution using MD simulation?

Dear all, I have performed MD simulation for different carbon nanotubes (CNTs) in water using NAMD software. Each CNT is solvated in a water box initially and MD is performed for each box. Is...

10 April 2018 5,259 7 View

UniProt database - can anyone help?

I need to know if the primary sequence provided by this database is trustworthy. I'm working on a transmembrane protein for which no complete x-ray structure is available. The point is that...

21 January 2014 5,777 10 View

How to model a Transmembrane protein while no experimental data is available for the relative orientation of ECD with respect to the TMD?

Hi everyone, I have a question about how to model a transmembrane protein composed of Extra-Cellular Domain (ECD) and Trans-Membrane Domain (TMD). No experimental data is available for the...

16 January 2014 6,701 5 View