[gmx-users] Different bonding energies for two almost the same systems

[Reza Salari]

Dear Gromacs Users,

I've been doing some calculations on methane-methane system in "bound" and "unbound" states to see how the energies compare. I set up everything almost the same between two system but I still get different bonding energies for two system. Here is what I did:

I first created two methanes separated for 4A to make my bound state. For unbound state, I increased the distance to 10A. The simulations were done in vacuum, all atoms were kept frozen and all non-bonding interactions were excluded (the coulombic and LJ energies are zero). So basically I have two system withe same atoms, bond lengths and angles. In each system, the two methanes don't "see" each other and are fixed in their positions. However I still get slightly different bonding energies for bound and unbound states. My question is, for this two systems, shouldn't the bonding energies (bond and angle energies) be same? Or more basically, isn't it expected that the potential energies for these two system be same at least for the first step?

I hope I am not missing something obvious. I attached mdp, pdb and log files. I also repeated the test with steep algorithm and also md dyanmics but the energies are still different.

Thank you in advance,

Reza Salari
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