[gmx-users] Exclusions in topology file seem not working for big systems

Reza Salari resal81 at yahoo.com
Thu Dec 3 17:59:12 CET 2009

Thanks Dr Hess.

I didn't get an error message when using grompp, then I think I didn't have too many exclusions.

I didn't know about using couple_type in this context before. If I get it correctly, if I want to exclude all non-bonding interactions inside a protein using couple_type, I must define it as follows in each mdp file for each lambda: (I need to decouple all the non-bonding intra molecular interactions for each lambdas):


If this is right, I will test it for my system which has ~7000 protein atoms. BTW I am still a little confused about the reported 1-4 energies while using exclusions, could you please explain this?. For my smaller system I got zero SR but non-zero 1-4 energies, even that the interactions between all the atoms were excluded. If I remove the pairs in topology file I would get no 1-4 term along with a different dV/dl value. So does it mean if I want to exclude all the intramolecular interactions I have to remove pairs? (my system is frozen and therefore I am not worried about the conformational change of the protein and also I am mainly interested in dV/dl values, which in this case is related to the electrostatic interaction of a residue with water as the charges on that residue being turned off).

Reza Salari

From: Berk Hess <gmx3 at hotmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thu, December 3, 2009 3:30:27 AM
Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems


If you really had too many exclusions you would get an error message.
So I just tested this.
I used the couple_moltype option to couple a 389 atom protein.
This generates exclusions between each protein atom and the 388 others.
All interactions are excluded correctly (and re-added as special 1-4's because
of the couple option).
So I don't understand what is going wrong in your case.


Date: Wed, 2 Dec 2009 09:31:03 -0800
From: resal81 at yahoo.com
Subject: Re: [gmx-users] Exclusions in topology file seem not working for big	systems
To: gmx-users at gromacs.org

Thanks for your response Dr van der Spoel.

Then there is a  limit on the number of atoms that can be defined in the exclusions section. My smaller system has 60 atoms and I used exclusions successfully for that, so I guess the limit might be a little more than 32.

Regarding the use of  energygrp_excl,it seems it does not work with PME. If I define the protein in the energygrp_excl group, grompp gives me this warning:

Can not exclude the lattice Coulomb energy between energy groups

Which I think means some of electrostatics is not going to be excluded between protein atoms. Is there a workaround for this? I think my last resort would be to run a simulation first with PME and without exclusions, and then rerunning it but this time by defining protein in the energygrp_excl  and using cut-off instead of PME. Then I guess I will be left with only protein-water interactions.

Reza Salari

From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wed, December 2, 2009 11:59:49 AM
Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems

Reza Salari wrote:
> Hi All,
> I seem to have a hard time to use exclusions in topology file. I have a relatively big system (~400 aa) that I am trying to calculate the difference in desolvation energy (dA) upon turning off charges on a specific residue using thermodynamics integration method. The system is a complex of two proteins and is frozen inside the box (for my project I need it to be frozen).¨

You can have max 32 exclusions per atom AFAIK.
However you can use energy_group_excluisions in the mdp file.
> To calculate the desolvation energy, I need to exclude all the non-bonding interactions among protein atoms, then the dA that I get corresponds to the desolvation energy (and doesn't include the lost interactions between mutated residue and the rest of protein). I couldn't use energygrp_excl in mdp file since I am using PME.  So I defined exclusions in topology file as follows (three-dot means that numbers continue to the last number):
> [ exclusions]
> 1 2 3 4 5 6 ... 6420
> 2 1 3 4 5 6 ... 6420
> 3 1 2 4 5 6 ... 6420
> ...
> ...
> 6420 1 2 3 ... 6419
> I used gmxdump to check that the exclusions were actually implemented, and it seems that they were.
> However when I use g_energy, I don't get zero energy for short range interactions. Here are the results of g_energy for simulations with and without exclusions:
>                    Coul-SR:Protein-Protein   LJ-SR:Protein-Protein     Coul-14:Protein-Protein     LJ-14:Protein-Protein
> no exclusions                -20277.6                                                    -13030.7                                                    37023.9                                                        7890.52
> using exclusions        -16221.2                                                    -10332.9                                                    37023.9                                                         7890.52
> I did the same test with a small system (~6 residue) and I did get zero SR interactions. While the exclusions work for my small system, I don't know why they seem not working for my bigger system. Am I missing something here or is there something like an implicit limit for the number of atoms that can be defined in the exclusion section of topology file?
> I appreciate any hint or help.
> Regards,
> Reza Salari

-- David.
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,      75124 Uppsala, Sweden
phone:    46 18 471 4205        fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org  http://folding.bmc.uu.se
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