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

Reza Salari resal81 at yahoo.com
Wed Nov 4 17:49:08 CET 2009

Thanks Mark for your response. 
I already did that and the energies are different there too. Actually I think it is reasonable for non-frozen test to have different bonding energies since the potential term is constantly changing but I don't understand why the potentials are different for frozen test?


From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wed, November 4, 2009 11:37:32 AM
Subject: Re: [gmx-users] Different bonding energies for two almost the same systems

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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