[gmx-users] Printing energies at every step of energy minimization

Hello, I am working on parameterizing a small molecule using GROMACS and am having issues during energy minimization. I want the program to output the potential energy at every step, except it only prints at the initial step. The program shows that it takes another 7 steps, although it does

[gmx-users] Syntax Error when Adding Ions to DNA/ligand complex

Hello GROMACS users, I am attempting to run a molecular dynamics simulation with DNA complexed with a small molecule. I have processed the molecule with ACPYPE, using the GAFF, and merged the topology files into a single topology file. However, when I attempt to use the “grompp” command

[gmx-users] Force Field for Small Molecule

Hello, I am working on a molecular dynamics simulation in GROMACS and am curious as to which force field will be the best to run a simulation on a small organic molecule containing carbon, nitrogen, oxygen and hydrogen. Through some research it seems that the general Amber force field (gaff)