OpenMM (MD) calculations crash during equilibration step

[Divya Matta]

Dear all,

I am running Molecular Dynamics simulations for wild-type (wt) Photosystem II (PSII) using OpenMM. The system files for OpenMM are generated using CHARMM-GUI. It ran without any error for wt. However, for mutant of PSII (generated by CHARMM-GUI), it crashes during minimization step(step 6) when I ran in OpenMM. Also, I am not sure why energy is increasing although I do not see any atoms clashing when I look the coordinate file for mutant PSII in vmd. Below is the output:

-bash-4.2$ cat step6.1_equilibration.out
Loading parameters

Initial system energy
-445147.27409367263 kJ/mol

Energy minimization: 5000 steps
899769944.7259064 kJ/mol

Generate initial velocities

MD run: 25000 steps

Please assist me.

Best Regards
Divya

[Ross Gunderson]

Can you provide more information? It isn't clear from your text why the system is crashing...
Is there an output from Python as to why it failed?