Hannah Burton

6 Questions 5 Answers 0 Followers

Questions related from Hannah Burton

GROMACS: Best restraint to keep ions out of the pore?

Hello everyone, I currently have a protein in a fully equilibrated membrane system. For the analysis I am running, I need to remove Na+ ions from the inside of the pore region. I would normally...

26 June 2024 4,569 4 View

The concentration of H+ after a buffer solution has been exhausted?

I have been trying to figure out how to calculate what the concentration of a [H+] would be after you have exhausted the concentration of a buffer solution to figure out what the proper voltage...

19 June 2023 6,124 1 View

How would I calculate the mass transport coefficient for protein-facilitated membrane transport?

Hello all, I have been trying to figure out how to calculate the mass transfer coefficient of a linear membrane system solvated within an aqueous box of unknown length. Transfer of 1 ion to the...

14 July 2022 5,995 0 View

Converging the Bulk ions in MD simulations?

I am currently running a umbrella sampling process where the calculation of some property is highly dependent on the positions of ions separated by a protein embedded in a membrane. However I have...

25 January 2022 3,619 0 View

How to add ions to an old DRUDE NAMD simulation?

Hello, I was passed an older simulation that was originally done in 2016. I no longer have any of the original input files and only have vmd modified DRUDE pdb files, its corresponding .xplor...

31 August 2021 3,150 1 View

Conversion from NAMD format to Gromacs?

Hi, I am looking to restart a simulation from NAMD to Gromacs using their initial system setup and apply a uniform electric field across it. I've been given NAMD files but cannot find a way to...

25 May 2021 4,059 3 View