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

[Reza Salari]

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). 

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
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