[gmx-users] Bond Energy question.

[Mark Abraham]

On Thu, Sep 11, 2014 at 9:24 AM, Dan Sponseller <gromacs at danpeg.com> wrote:

> Hello.
>
> 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?


Not true. See
http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy


> The G96Bond energy should just be reporting the interaction between bonded
> atoms, correct?
>

Yes

Mark


> Thanks for any insight.
>
> Dan Sponseller
> PhD student
> George Mason University
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