[gmx-users] Exclusions in topology file seem not working for big systems
resal81 at yahoo.com
Wed Dec 2 18:31:03 CET 2009
Thanks for your response Dr van der Spoel.
Then there is a limit on the number of atoms that can be defined in the exclusions section. My smaller system has 60 atoms and I used exclusions successfully for that, so I guess the limit might be a little more than 32.
Regarding the use of energygrp_excl,it seems it does not work with PME. If I define the protein in the energygrp_excl group, grompp gives me this warning:
Can not exclude the lattice Coulomb energy between energy groups
Which I think means some of electrostatics is not going to be excluded between protein atoms. Is there a workaround for this? I think my last resort would be to run a simulation first with PME and without exclusions, and then rerunning it but this time by defining protein in the energygrp_excl and using cut-off instead of PME. Then I guess I will be left with only protein-water interactions.
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wed, December 2, 2009 11:59:49 AM
Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems
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.
> Reza Salari
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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