Akiko Mendoza

6 Questions 9 Answers 0 Followers

Questions related from Akiko Mendoza

How can I to compute a distance between a plane and a point in GROMACS?

I have a coarse-grain molecular dynamic performed in Gromacs. I am interested, in computing the distance between an atom (bead) and a group of atoms (beads), that we can see as a plane. Thanks...

12 August 2021 6,103 4 View

How can I to compute the distance between a coarse-grain bead and a group of coarse-grain beads in a molecular dynamic?

I have a coarse-grain molecular dynamic performed in Gromacs. I am interested, in computing the distance between an atom (bead) and a group of atoms (beads). That is to say, I want the distance...

14 July 2021 2,383 11 View

How I can insert to a bilayer complex more lipids?

I constructed with insane.py a system with three diferent lipids (DOPC, DOPS, POP2) and a protein with myristoil. The insane.py script insert the protein in the membrane but in the place of the...

18 June 2020 3,897 0 View

Can anyone, suggest a tutorial to generate Martini protein topology and structure files based on an atomistic structure file?

I have a membrane protein myristoylated attached in a DPPC membrane with water. I want to generate a coarse-grain system with this PDB. My problem is that I do not find the correct instructions to...

01 May 2020 8,744 1 View

How to fix ions in a protein during MD visualization?

I performed a molecular dynamics in GROMACS 2019.2 of a protein with zinc fingers (50 amino acids). When I visualize it with Chimera the ions jump everywhere.

06 April 2020 9,531 7 View

How can I implement a script in Chimera?

I want to evaluate several structures, the distances between two atoms.

22 March 2020 8,610 3 View