<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:12pt;color:#000000;"><div>Hi All,<br><br>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). <br><br>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):<br><br>[ exclusions]<br>1 2 3 4 5 6 ... 6420<br>2 1 3 4 5 6 ... 6420<br>3 1 2 4 5 6 ... 6420<br>...<br>...<br>6420 1 2 3 ... 6419<br><br>I used gmxdump to check that the exclusions were actually implemented, and it seems that they were.<br><br>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:<br><br><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;"> Coul-SR:Protein-Protein LJ-SR:Protein-Protein Coul-14:Protein-Protein LJ-14:Protein-Protein</span><br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier New,courier,monaco,monospace,sans-serif;">no exclusions</span>
-20277.6 -13030.7 37023.9 7890.52 <br style="font-family: Courier New,courier,monaco,monospace,sans-serif;"><span style="font-family: Courier
New,courier,monaco,monospace,sans-serif;">using exclusions</span> -16221.2 -10332.9 37023.9 7890.52<br style="font-family: Courier
New,courier,monaco,monospace,sans-serif;"><br><br>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? <br><br>I appreciate any hint or help.<br><br>Regards,<br>Reza Salari<br></div>
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