<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:12pt"><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;">Thanks for your response.<br><br>I see that what I want to do is a little bit unusual. It is part of a bigger picture that also include implicit water calculations and the main goal is to look into the effects of water models on the results, not necessarily trying to reproduce the experimental results. I have gotten some encouraging results for smaller systems and now I want to try some bigger ones. <br><br>The good news is that I've found a workaround for calculating desolvation energy which seems easier and cleaner than using exclusions (it involves using dV/dlambda calculations directly), so it seems that I don't need to use exclusions anymore.<br><br>Regards,<br>Reza Salari<br><br><br><br><div style="font-family: times new roman,new
york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Berk Hess <gmx3@hotmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Fri, December 4, 2009 8:01:34 AM<br><b><span style="font-weight: bold;">Subject:</span></b> RE: [gmx-users] Exclusions in topology file seem not working for big systems<br></font><br>
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Hi,<br><br>I don't know.<br>I have not understood what you want to do.<br>On the physical level, there is no distinction between intra-molecular bonded<br>and non-bonded interactions. So this makes me suspect that what you are<br>trying to do is incorrect, independently of if you remove the 1-4's or not.<br><br>Berk<br><br><hr id="stopSpelling">Date: Thu, 3 Dec 2009 10:40:08 -0800<br>From: resal81@yahoo.com<br>Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems<br>To: gmx-users@gromacs.org<br><br>
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</style><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;"><div>Thank you very much Dr Hess.<br><br>Then I guess I have to test my rerun workaround that I mentioned for my system. <br><br>About 1-4 interactions in general, could you a little bit about 1-4 energies while using exclusions please? I hope I am not missing something obvious. The main thing that I am not sure about is if I want to exclude all non-bonding interactions inside a small molecule, do I need to remove [pairs] when adding the [exclusions]? I am using OPLSAA.<br><br>Regards,<br>Reza Salari<br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Berk Hess <gmx3@hotmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users
<gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thu, December 3, 2009 12:06:53 PM<br><b><span style="font-weight: bold;">Subject:</span></b> RE: [gmx-users] Exclusions in topology file seem not working for big systems<br></font><br>
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Hi,<br><br>I think that for your problem the couple option is not useful.<br>It does exactly the opposite. I removes all interactions of the selected molecule type with the rest of the system<br>and transform all interactions within the molecule by "vacuum" non-cutoff LJ and Coulomb interactions.<br>(which end up in special 1-4 energy terms).<br><br>Berk<br><br><hr id="ecxstopSpelling">Date: Thu, 3 Dec 2009 08:59:12 -0800<br>From: resal81@yahoo.com<br>Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems<br>To: gmx-users@gromacs.org<br><br>
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</style><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;"><div>Thanks Dr Hess.<br><br>I didn't get an error message when using grompp, then I think I didn't have too many exclusions.<br><br>I didn't know about using couple_type in this context before. If I get it correctly, if I want to exclude all non-bonding interactions inside a protein using couple_type, I must define it as follows in each mdp file for each lambda: (I need to decouple all the non-bonding intra molecular interactions for each lambdas):<br><br>couple_moltype=protein<br>couple_lambda0=none<br>couple_lambda1=none<br>couple-intramol=none<br><br>If this is right, I will test it for my system which has ~7000 protein atoms. BTW I am still a little confused about the reported 1-4 energies while using exclusions, could you please explain this?. For my smaller system I got zero SR but non-zero 1-4
energies, even that the interactions between all the atoms were excluded. If I remove the pairs in topology file I would get no 1-4 term along with a different dV/dl value. So does it mean if I want to exclude all the intramolecular interactions I have to remove pairs? (my system is frozen and therefore I am not worried about the conformational change of the protein and also I am mainly interested in dV/dl values, which in this case is related to the electrostatic interaction of a residue with water as the charges on that residue being turned off).<br><br>Regards,<br>Reza Salari<br><br><br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Berk Hess <gmx3@hotmail.com><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for
GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Thu, December 3, 2009 3:30:27 AM<br><b><span style="font-weight: bold;">Subject:</span></b> RE: [gmx-users] Exclusions in topology file seem not working for big systems<br></font><br>
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Hi,<br><br>If you really had too many exclusions you would get an error message.<br>
So I just tested this.<br>I used the couple_moltype option to couple a 389 atom protein.<br>This generates exclusions between each protein atom and the 388 others.<br>All interactions are excluded correctly (and re-added as special 1-4's because<br>of the couple option).<br>So I don't understand what is going wrong in your case.<br><br>Berk<br><br><hr id="ecxecxstopSpelling">Date: Wed, 2 Dec 2009 09:31:03 -0800<br>From: resal81@yahoo.com<br>Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems<br>To: gmx-users@gromacs.org<br><br>
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</style><div style="font-family: Courier New,courier,monaco,monospace,sans-serif; font-size: 12pt;"><div style="font-family: Courier New,courier,monaco,monospace,sans-serif; font-size: 12pt;"><span style="font-family: arial,helvetica,sans-serif;">Thanks for your response Dr van der Spoel.<br><br></span><span style="font-family: arial,helvetica,sans-serif;">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.<br><br>Regarding the use of </span> energygrp_excl,<span style="font-family: arial,helvetica,sans-serif;">it seems it does not work with PME. If I define the protein in the </span>energygrp_excl <span style="font-family: arial,helvetica,sans-serif;">group, grompp gives me this warning:<br></span><pre style="">Can not exclude the lattice Coulomb energy between energy<br><br>
groups<br></pre><br> <span style="font-family: arial,helvetica,sans-serif;">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 </span>energygrp_excl<span style="font-family: arial,helvetica,sans-serif;"> and using cut-off instead of PME. Then I guess I will be left with only protein-water interactions.<br><br>Regards,<br>Reza Salari<br></span><br><span style="font-family: arial,helvetica,sans-serif;"><br></span><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> David van der Spoel <spoel@xray.bmc.uu.se><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users
<gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wed, December 2, 2009 11:59:49 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Exclusions in topology file seem not working for big systems<br></font><br>
Reza Salari wrote:<br>> 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>You can have max 32 exclusions per atom AFAIK.<br>However you can use energy_group_excluisions in the mdp file.<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>> Coul-SR:Protein-Protein LJ-SR:Protein-Protein Coul-14:Protein-Protein LJ-14:Protein-Protein<br>> no exclusions -20277.6
-13030.7 37023.9 7890.52<br>> using exclusions -16221.2 -10332.9 37023.9
7890.52<br>> <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>> <br><br><br>-- David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Professor of Biology<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511
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