[gmx-users] Positive Potential Energy.

[Dan Sponseller]

Hello everyone.

I am still fairly new to gromcs but I have researched this well.

I am getting a positive potential energy (my bond energy is always positive) no matter how long I run my simulation. I also get this when doing minimizations. Even just one molecule set at know minimum conformation. 

I am running in vacuo with no pbc. I have read on the mail list that in vacuo can produce this? This doesn’t make sense as the molecule should fly apart with always positive PE.

I have tried gromos ff and opsla ff. Both do this. A colleague of mine also  gets this with his simulations although he reports negative potential when solvated.

Any help would be appreciated or any explanation on how to interpret gromacs output on this.

I would question gromacs’ abilities if it cannot give a reasonable potential energy for a simple system.

Daniel Sponseller
PhD student
George Mason University