[gmx-users] Vacuum versus Water Simulation

[Johnny Lu]

Dear Users,

Hi.

Alanine peptide was simulated in water and in vacuum under NVE ensemble.

The magnitude of harmonic components were similar in both simulations (as
shown by Fourier transformation).

Is this normal?

I thought without the damping by water, the vacuum simulation would have a
much stronger harmonic component of motion (which is not the case).

>From rmsd, I think the peptide still moved in the vacuum simulation.

Thank you.