[gmx-users] Wall potential for a membrane simulation

Hello, I would like to simulate a membrane system with two walls, one at the bottom of my box at z=0 and one at the top, using the gromos53a6 forcefield (GROMACS version 4.5.5). My testing system consists of a membrane in the middle, water and sodium ions (40xNa+) above the membrane and water

[gmx-users] Wall potential for a membrane-simulation

  Hi everyone! I'm new to Gromacs and trying to simulate a membrane system with two walls, one at the bottom of my box at z=0 and one at the top, using the gromos53a6 forcefield (GROMACS version 4.5.5). My testing system consists of a membrane in the middle, water and sodium ions (40) abov

[gmx-users] Wall potential

Hi Gomacians, I want to use implicit wall. I set the mdp parameters as follows. nwall= 2 wall_type= 9-3 wall_r_linpot= 1 wall_atomtype= Au Au wall_density = 58.01 58.01 wall_ewald_zfac = 3 Also set LJ p

[gmx-users] Wall Potential

Hi all, I am trying to simulate multiple (2 or 3) tetrapeptides in a cage with Gromacs. However, I would like to constrain the peptides to the centre of the box by enforcing a wall potential in which each of the atoms of the peptide feels a repulsive potential with respect to the edge of the box