[gmx-users] Test particle insertion for all atom force field

Hi everyone, I want to calculate excess chemical potential for some molecules in water. I found a tutorial on this but it was on methane (united atom). The insertion of the test particle requires that it is included as the last atom in the .gro file with coordinate 0.000 0.000

[gmx-users] All atom coordinates for Test Particle Insertion

Hi everyone, I want to calculate excess chemical potential for some molecules in water. I found a tutorial on this but it was on methane (united atom). The insertion of the test particle requires that its included in the .gro file with coordinate 0.000 0.000 0.000. This works

[gmx-users] g_spatial Problem

Hi everyone, I want to generate the spatial distribution function of Molecule A around molecules B. I have 48 molecules of A and 200 molecules of B in a cubic box and I want to find the spatial distribution of B around A in the first shell of B ( about 5A away from A base

[gmx-users] Non-uniform structure of water around H2S

Dear Gromacs users, I am trying to understand the structure of H2O around one H2S molecule in a system of H2S-H2O confined in silica pore. Looking at the equilibrated system of the simulation snapshot, the arrangement of water molecules around each H2S is non-uniform and as a result, parame