[gmx-users] Exclusions in topology file seem not working for big systems
resal81 at yahoo.com
Wed Dec 2 17:32:18 CET 2009
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):
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.
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