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?
Reza ________________________________ From: Mark Abraham <mark.abra...@anu.edu.au> To: Discussion list for GROMACS users <gmx-users@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. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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