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).ยจ
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
sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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