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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