Bruno Santos

6 Questions 7 Answers 0 Followers

Questions related from Bruno Santos

How can I set the distance between peptide and bilayer using Packmol?

I still find Packmol very tricky with parameters. I have two pdb files, one with a pre-quilibrated bilayer and one with the peptide of interest. How can I create a system with three copies of the...

30 April 2024 8,216 1 View

How to calculate the solute concentration in molecular dynamics simulation?

I am trying to calculate how many SDS molecules I need in a MD box to achieve a specific concentration (ex: 1M). My first doubt is if I use the box volume or the quantity of water molecules, for...

17 April 2024 2,004 2 View

Why Waddell's method for peptide concentration calculation is the way it is?

The 1956 paper A simple ultraviolet spectrophotometric method for the determination of protein is constantly referenced as the one who provided a method for peptide concentration calculation that...

09 June 2023 924 2 View

Someone has a TEE-REX simulation pipeline/tutorial?

I am trying to implement a REX simulation on gromacs to analyze my peptide's folding, and the work of Kubitzki and de Groot (2008) has called my attention to TEE-REX simulation. Peharps the...

13 December 2022 3,830 0 View

How to anchor a peptide in the surface of a bilayer membrane using GROMACS?

I'd like to put the peptide molecule on the surface of a membrane, instead of inside, to observe affinity and capacity of trespassing the bilayer barrier. How can I do that on GROMACS?

06 June 2019 2,340 4 View

Why it is so hard to observe peptide folding in Molecular Dynamics and how to overcome it?

I work with peptide-bilayer interactions and I have tried a few strategies to observe the partitioning and folding of peptides, however without good results. If the problem is sampling, Replica...

01 January 1970 3,753 7 View