[gmx-users] Bond Energy question.

Dan Sponseller gromacs at danpeg.com
Thu Sep 11 09:25:07 CEST 2014


I have completed a simulation with two polyethylene glycol (PEG) molecules and then minimized the final conformation. As a demonstration that the two molecules wish to stick together, I separate the two molecules manually and run a single minimization step. I inspect the energy log file since it reports the energies at step zero. I show that the Potential energy is higher in the separated molecules which completes the demonstration.

However, I also notice that the G96Bond energy is almost double. Since the atoms within each molecule have not moved relative to each other at step zero, should not the bond energy not have changed? The G96Bond energy should just be reporting the interaction between bonded atoms, correct?

Thanks for any insight.

Dan Sponseller
PhD student
George Mason University

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