Movement of the molecules during energy minimization

[mjm91]

Dear gromacs users,

I am performin the energy minimization (with steepest descents algorithm) in gromacs for a system containing an organic molecule at the center of the simulation box solvated by a binary mix of solvents. After I performed the energy minimization, when I visualize the energy-minimized gro file on VMD, I see that the organic molecule (which was at the center of the box before EM) has been shifted to the edge of the simulation box, I did’nt encounter any error messages. Is it a visual artificat due to PBC effects as EM step simply modifies the internal degrees of freedom instead of moving a molecule completely. Any explanation would be much appreciated

[obZehn]

Hi @mjm91,

@mjm91

EM step simply modifies the internal degrees of freedom instead of moving a molecule completely.

What do you mean? If you are using the standard steepest descent method, then you are moving the atoms aiming for a configuration at lower potential energy.

Concerning the movement of the whole molecule, generally EM results in minor displacements ‘on the spot’. Have you tried to rebuild the box with gmx trjconv both before and after EM? They should roughly be the same.