Zeynab Mohammad Hosseini Naveh

10 Questions 20 Answers 0 Followers

Questions related from Zeynab Mohammad Hosseini Naveh

How to calculate the adsorption energy for a weak interaction using MD simulation?

Dear All, I have an amino acid interacting weak with a CNT. During the standard MD it adsorbs, desorbs and then re-adsorbs on the CNT surface. Which method does suits to calculate the adsorption...

01 January 2019 4,463 4 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...

05 May 2018 4,685 4 View

How to create an infinite graphene sheet?

Dear all, I want to run the molecular dynamics simulation of an infinite graphene sheet solvated in water using NAMD code. I don't know how to create an infinite sheet with it's periodic images....

05 May 2018 2,413 9 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...

04 April 2018 5,012 8 View

When the Zwitterion structure of amino acid turns into the neutral form?

Dear all, I read somewhere that the Zwitterion form of amino acid (AA) is observed in the physiological condition. The structure of AA (in Zwitterion form) which is adsorbed on a nano sheet (NSH)...

04 April 2018 1,398 4 View

How deal with the MD simulation of two interacting molecules in the presence of Periodic Boundary Conditions (PBCs)?

Hi Everybody, Wish somebody help me to understand the following situation: Consider the MD simulation of two interacting molecule (first one on the left and the second one on the right) in a unit...

09 September 2017 8,491 9 View

How can I restart a TranSiesta job from the previous run?

Dear all, I'm new in Siesta and TranSieta. However, I asked some of my friends,having experience with these software, and they didn't know the answers. So I didn'thave any other choice except for...

06 June 2016 3,508 1 View

Why do propka3 (only protein) and propka 3.1 (protein and ligand) produce different results?

I want to predict the protonation states of Histidine in my protein and I don't have any ligand. As long as I try Propka 3 (only protein) and Propka 3.1 (protein and ligand), I receive different...

02 February 2014 1,234 8 View

Can anyone help with protein-lipid interface hydration?

I ran the NPT simulation for a membrane protein embedded in the lipid bilayer and I see that water is penetrating from one small cavity, located at the lipid-protein interface, into the membrane...

02 February 2014 5,745 2 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...

01 January 2014 7,308 11 View