[gmx-users] constraint pull code / gromacs 5.0.4

[Alex]

CA> My nanoparticles (Radius = 1nm) are made of alumina and
CA> the force field was CLAYFF

I assume you realize that simulating metals within the GMX-like paradigm
is physically incorrect. In short, your particles are not metallic,
but crystalline clusters with vdw surface.
That in itself, however, should not cause what you're observing.

Let's try to diagnose it one step at a time. Can you please look at
the pdb and post the first-neighbor interatomic AL-AL distance?

Also, please post the bond length and the equilibrium angle in the forcefield parameters.

Is it possible to simulate one of these nanoparticles in vacuum (no
pull code, no solvent, NVE) and look at the kinetic/potential energies
of the system?

Alex