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

[David van der Spoel]

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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