[gmx-users] Different bonding energies for two almost the same systems
Mark.Abraham at anu.edu.au
Wed Nov 4 17:37:32 CET 2009
Reza Salari wrote:
> 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.
Try turning off freeze groups.
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