[gmx-users] long range interactions depend on bonds ?

Berk Hess gmx3 at hotmail.com
Fri Jul 9 17:23:06 CEST 2004

>From: Michael Brunsteiner <mbx0009 at yahoo.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-developers at gromacs.org
>CC: gmx-users at gromacs.org
>Subject: [gmx-users] long range interactions depend on bonds ?
>Date: Fri, 9 Jul 2004 07:59:58 -0700 (PDT)
>Dear all,
>I saw some quite unexpected results from Gromacs
>runs today, and would appreciate if somebody could
>tell whats going on here ...
>I do MD with a system containing three energygroups, A, B and C.
>One of the groups, A, contains only frozen atoms.
>To get the long range contributions to the interaction
>energies A-B, B-C, etc I use tpbconv, setting up six reruns
>with the charges set to zero for each group and each
>combination of two groups (as previously suggested in this list)
>this seems to work fine.
>For some reason I repeated a couple of these simulations
>and due to some mistake I ended up with a number of bonds
>bewteen atoms in group A being defined in the topology file
>(In the first set of runs these bonds were not there
>which shouldn't make a difference since all these atoms are
>frozen anyway)
>what I see is the following:
>the long range contribution ELR to the interaction energies
>depends on whether these bonds are there or not, and most
>notably, not only the ELR for A-A interactions but also those
>for A-B and A-C depend on the bonding between atoms in A.
>I this supposed to be like that ?
>Electrostatic short range interactions between two bonded atoms are
>excluded, but why would the bond affect also the long range interactions ?
>And even stranger why should it affect long range interaction energies
>between two entirely different groups (i.e. molecules) ???

I just replied to the same mail on the developers list.
Could you please send mails to one list only (gmx-users in this case)?

Do you use constraints?
When constraints are present atoms might not be completely frozen,
as they also need to satisfy the constraints.


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