[gmx-users] Exclusions and pairs
Dear Gromacs users: Am I right assuming that [exclusions] do not affect the interactions defined by [pairs]? This seems to be implied from the note in section 5.3.4 in the manual: Note that one should add exclusions for all atom pairs participating in pair interactions type 3, otherwise such pairs will also end up in the normal neighbor lists. I think, however, that it can be confusing given the overall concept: [exclusions] removes non-bonded interactions, and [pairs] defines non-bonded interactions. One could think that pairs would be excluded too. May I suggest a more explicit statement to be added to the 5.4 sections (that [exclusions] do not affect [pairs]? Ignacio -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Exclusions and pairs
On 1/10/13 11:14 AM, Ignacio Fernández Galván wrote: Dear Gromacs users: Am I right assuming that [exclusions] do not affect the interactions defined by [pairs]? This seems to be implied from the note in section 5.3.4 in the manual: Note that one should add exclusions for all atom pairs participating in pair interactions type 3, otherwise such pairs will also end up in the normal neighbor lists. I think, however, that it can be confusing given the overall concept: [exclusions] removes non-bonded interactions, and [pairs] defines non-bonded interactions. One could think that pairs would be excluded too. May I suggest a more explicit statement to be added to the 5.4 sections (that [exclusions] do not affect [pairs]? Pairs are bonded interactions. http://lists.gromacs.org/pipermail/gmx-users/2009-July/043326.html The type 3 pair you're referring to has a very specific use in free energy calculations, and that section of the manual has actually been re-written for version 4.6 and the usage changed to require a [pairs_nb] directive to indicate special nonbonded interactions in that case. I think the newer explanation is slightly clearer than before. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Exclusions in TIP4P
Hi all, In the OPLS-AA tip4p.itp file I see: [ moleculetype ] ; molname nrexcl SOL 2 and [ exclusions ] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 If bonded interactions are included (FLEXIBLE defined), interactions between atoms 1, 2, 3 are already excluded, right? And is it needed to have both the n-m and m-n exclusions listed? Wouldn't it be the same with this?: [ exclusions ] 1 2 3 4 2 3 4 3 4 Thanks, Ignacio -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] exclusions
Hi all
I am cheking the non binary version topol.tpr form grompp and I was
wondering what the following format for the exclusion section signifies?
excls:
nr=228
nra=1920
excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16}
excls[1][13..25]={0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 15}
Also I take it, that this is a result of nrexcl =3
Cheers
Gavin
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Re: [gmx-users] exclusions
Regarding my earlier post- If someone could confirm.
Taking into account that atom indices start from zero.
Then excls[0] = exclusions centred around atom 1.
[0..12] = there are 13 exclusions each one labelled form 0-12.
I then assume that you read the exclusions with respect to atom 0
(actual index =1)
In the next set do you read the exclusion with respect to atom 1 (actual
index =2).
and so on
Many thanks in advance
Gavin
Gavin Melaugh wrote:
Hi all
I am cheking the non binary version topol.tpr form grompp and I was
wondering what the following format for the exclusion section signifies?
excls:
nr=228
nra=1920
excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16}
excls[1][13..25]={0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 15}
Also I take it, that this is a result of nrexcl =3
Cheers
Gavin
--
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Re: [gmx-users] exclusions
On 12/05/2011 2:43 AM, Gavin Melaugh wrote:
Regarding my earlier post- If someone could confirm.
Taking into account that atom indices start from zero.
Then excls[0] = exclusions centred around atom 1.
[0..12] = there are 13 exclusions each one labelled form 0-12.
I then assume that you read the exclusions with respect to atom 0
(actual index =1)
I doubt it. I think each particle excludes itself in the list. Make a
simple system where you can compute the exclusions by hand and see what
the data structure is doing. Then vary it until you're happy with your
deductions.
Mark
In the next set do you read the exclusion with respect to atom 1 (actual
index =2).
and so on
Many thanks in advance
Gavin
Gavin Melaugh wrote:
Hi all
I am cheking the non binary version topol.tpr form grompp and I was
wondering what the following format for the exclusion section signifies?
excls:
nr=228
nra=1920
excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 16}
excls[1][13..25]={0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 15}
Also I take it, that this is a result of nrexcl =3
Cheers
Gavin
--
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[gmx-users] exclusions for a specific model
Dear GROMACS users, I created a custom topology file to define a molecule composed of 5 sites. Two sites are real massive sites (but for them C6=C12=0 and their charge is 0, hence they do not interact with sites of same type on other molecules), while remaining three sites are virtual sites. Two of these virtual sites carry a charge (but C6=C12=0), while the third one has no charge and interact with other virtual sites of same type through VdW interactions. With this topology real sites do not interact with other real sites but they are used only to carry a given mass. My question is: is it possible to exclude these real sites from non-bonded forces calculations (and neighbors search) to speedup simulations? unless having C6=C12=0 and 0 charge for real sites they are automatically excluded... thanks for your help in advance, Cristiano Cristiano De Michele, Ph.D. Department of Physics Tel. : +390649913524 University of Rome La SapienzaFax : +39064463158 Piazzale Aldo Moro, 2 I-00185 Roma - Italy homepage: http://pacci.phys.uniroma1.it/ -- Shoot for the moon. Even if you miss, you'll land among the stars. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] exclusions for a specific model
On 17/03/2010 9:20 PM, Cristiano De Michele wrote: Dear GROMACS users, I created a custom topology file to define a molecule composed of 5 sites. Two sites are real massive sites (but for them C6=C12=0 and their charge is 0, hence they do not interact with sites of same type on other molecules), while remaining three sites are virtual sites. Two of these virtual sites carry a charge (but C6=C12=0), while the third one has no charge and interact with other virtual sites of same type through VdW interactions. With this topology real sites do not interact with other real sites but they are used only to carry a given mass. My question is: is it possible to exclude these real sites from non-bonded forces calculations (and neighbors search) to speedup simulations? unless having C6=C12=0 and 0 charge for real sites they are automatically excluded... I suspect GROMACS does this check-for-zero already. If you look at the FLOP summary at the end of a .log file, it tells you how many flops were spent in various inner loops doing some combination of LJ and Coulomb. You should see a pattern characteristic of your system. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Exclusions in topology file seem not working for big systems
Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org 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. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@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 -13030.737023.9 7890.52 using exclusions-16221.2 -10332.937023.9 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 4205fax: 46 18 511 755 sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Exclusions in topology file seem not working for big systems
Thanks Dr Hess. I didn't get an error message when using grompp, then I think I didn't have too many exclusions. 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): couple_moltype=protein couple_lambda0=none couple_lambda1=none couple-intramol=none 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). Regards, Reza Salari From: Berk Hess g...@hotmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, December 3, 2009 3:30:27 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org 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. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@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
RE: [gmx-users] Exclusions in topology file seem not working for big systems
Hi, I think that for your problem the couple option is not useful. It does exactly the opposite. I removes all interactions of the selected molecule type with the rest of the system and transform all interactions within the molecule by vacuum non-cutoff LJ and Coulomb interactions. (which end up in special 1-4 energy terms). Berk Date: Thu, 3 Dec 2009 08:59:12 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks Dr Hess. I didn't get an error message when using grompp, then I think I didn't have too many exclusions. 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): couple_moltype=protein couple_lambda0=none couple_lambda1=none couple-intramol=none 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). Regards, Reza Salari From: Berk Hess g...@hotmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, December 3, 2009 3:30:27 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org 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. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@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
Re: [gmx-users] Exclusions in topology file seem not working for big systems
Thank you very much Dr Hess. Then I guess I have to test my rerun workaround that I mentioned for my system. 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. Regards, Reza Salari From: Berk Hess g...@hotmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, December 3, 2009 12:06:53 PM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, I think that for your problem the couple option is not useful. It does exactly the opposite. I removes all interactions of the selected molecule type with the rest of the system and transform all interactions within the molecule by vacuum non-cutoff LJ and Coulomb interactions. (which end up in special 1-4 energy terms). Berk Date: Thu, 3 Dec 2009 08:59:12 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org Thanks Dr Hess. I didn't get an error message when using grompp, then I think I didn't have too many exclusions. 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): couple_moltype=protein couple_lambda0=none couple_lambda1=none couple-intramol=none 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). Regards, Reza Salari From: Berk Hess g...@hotmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, December 3, 2009 3:30:27 AM Subject: RE: [gmx-users] Exclusions in topology file seem not working for big systems Hi, If you really had too many exclusions you would get an error message. So I just tested this. I used the couple_moltype option to couple a 389 atom protein. This generates exclusions between each protein atom and the 388 others. All interactions are excluded correctly (and re-added as special 1-4's because of the couple option). So I don't understand what is going wrong in your case. Berk Date: Wed, 2 Dec 2009 09:31:03 -0800 From: resa...@yahoo.com Subject: Re: [gmx-users] Exclusions in topology file seem not working for big systems To: gmx-users@gromacs.org 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. Regards, Reza Salari From: David van der Spoel sp...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@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
[gmx-users] Exclusions for aromatic residues
Hi, In .rtp file of a GROMOS 96 force field (ffG43a1.rtp for example), exclusions seem to be listed only for aromatic residues such as TYR, HIS, and TRP. Why is that so? Sanghwa Han ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Exclusions for aromatic residues
한상화 wrote: Hi, In .rtp file of a GROMOS 96 force field (ffG43a1.rtp for example), exclusions seem to be listed only for aromatic residues such as TYR, HIS, and TRP. Why is that so? normally they are generated (chapter 4) but one can define extra exclusions. interactions within rings usualy just work to deform the rings which is undesired therefore they are turned off. Sanghwa Han ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
