[gmx-users] Atom Types in ffbonded.itp
Hello I want to write my parameters in the ffbonded.itp file in the CHARMM27 force field folder. I wrote my atom types in this file. This atom types are defined by me in atomtypes.dat grompp gives me an error Fatal error: Unknown bond_atomtype for all my atom types. Do I have to declare that atom types somewhere else than in atomtypes.dat? What is the problem? Greetings Lara -- 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] Atom Types in ffbonded.itp
On 5/14/12 4:38 PM, Lara Bunte wrote: Hello I want to write my parameters in the ffbonded.itp file in the CHARMM27 force field folder. I wrote my atom types in this file. This atom types are defined by me in atomtypes.dat There is no atomtypes.dat that is read by any Gromacs program, and atomtypes.atp is not relevant here. grompp gives me an error Fatal error: Unknown bond_atomtype for all my atom types. Do I have to declare that atom types somewhere else than in atomtypes.dat? All atom types need to be present in ffnonbonded.itp, with their parameters defined there. The atom types present in ffnonbonded.itp can then be used in bonded interactions defined in ffbonded.itp. -Justin -- Justin A. Lemkul, Ph.D. 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] Atom types for phosphate group in OPLS-AA force field
Dear Gromacs users, I am here requesting your help with regards to the editing of the OPLS-AA force field, and more specifically, the choice of the atom types. I have added an entry for the molecule CABP to the .rtp and .hdb files. I can run pdb2gmx, genbox and editconf without getting any error. However, when I run grompp, I receive the following errors: ERROR 1 [file 1RBO_Protein_chain_A.itp, line 15054]: No default Bond types ERROR 78 [file 1RBO_Protein_chain_M.itp, line 47276]: No default Angle types ERROR 82 [file 1RBO_Protein_chain_M.itp, line 66639]: No default Ryckaert-Bell. types (there are 160 of those). From what I could see in this mailing list, it seems the error comes from the choice of the atom types for the phosphate groups. I have tried several of them which seemed to make sense, but none of them allowed to remove all the errors. The end of the chain is something like: O | (...)--CH2--O--P--O--H | O (details of the whole molecule here: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO ) The problem is about the atom type of the -OH group at the end. Here are the entries from the .atp file which I thought were relevant: opls_445 30.97376 ; P in MeOPO3--, MeOPO3H2 opls_446 15.99940 ; O= in MeOPO3--, MeOPO3H2 opls_447 15.99940 ; OMe in MeOPO3--, MeOPO3H2 methyl phosphate opls_448 12.01100 ; C in MeOPO3--, MeOPO3H2 6-31+G* CHELPG opls_449 1.00800 ; H in MeOPO3--, MeOPO3H2 I chose opls_445 for the P, opls_446 for the 3 oxygens, and opls_449 for the hydrogen. Apparently, I got it wrong for the oxygen and the hydrogen of the OH group, at least. Unless the error actually comes from something else... So my question is the following: Have I done something wrong about the atom types? If so, does anyone know which atom type I should choose? Details of my rtp entry: [ CAP ] [ atoms ] P1 opls_445 1.539429 1 O1P opls_446 −0.818751 1 O2P opls_446 −0.899293 1 HO2P opls_449 0.429028 1 O3P opls_446 −0.895147 1 O1 opls_447 −0.772438 2 C1 opls_448 0.022084 3 HC11 opls_449 0.176920 3 HC12 opls_449 0.139342 3 C2 opls_159 0.146383 4 O2 opls_154 −0.883774 4 HO2 opls_155 0.527657 4 C opls_271 0.815849 5 O6 opls_271 −0.766517 5 O7 opls_272 −0.771422 5 C3 opls_158 0.142583 6 HC3 opls_140 0.107158 6 O3 opls_154 −0.817159 6 HO3 opls_155 0.471262 6 C4 opls_158 0.184473 7 HC4 opls_140 0.164192 7 O4 opls_154 −0.822792 7 HO4 opls_155 0.498509 7 C5 opls_448 0.038563 8 HC51 opls_449 0.143027 8 HC52 opls_449 0.135804 8 O5 opls_447 −0.730025 9 P2 opls_445 1.526672 10 O4P opls_446 −0.866625 10 O5P opls_446 −0.810148 10 HO5P opls_449 0.521464 10 O6P opls_446 −0.876311 10 [ bonds ] HO2P O2P O1P P1 O2P P2 O3P P1 P1 O1 O1 C1 C1 HC11 C1 HC12 C1 C2 C2 O2 O2 HO2 C2 C C O6 C O7 C2 C3 C3 O3 C3 HC3 O3 HO3 C3 C4 C4 HC4 C4 O4 O4 HO4 C4 C5 C5 HC51 C5 HC52 C5 O5 O5 P2 P2 O4P P2 O5P P2 O6P O5P HO5P Thank you very much in advance! Antoine -- 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] Atom types for phosphate group in OPLS-AA force field
On 4/26/12 7:45 AM, Delmotte, Antoine wrote: Dear Gromacs users, I am here requesting your help with regards to the editing of the OPLS-AA force field, and more specifically, the choice of the atom types. I have added an entry for the molecule CABP to the .rtp and .hdb files. I can run pdb2gmx, genbox and editconf without getting any error. However, when I run grompp, I receive the following errors: ERROR 1 [file 1RBO_Protein_chain_A.itp, line 15054]: No default Bond types ERROR 78 [file 1RBO_Protein_chain_M.itp, line 47276]: No default Angle types ERROR 82 [file 1RBO_Protein_chain_M.itp, line 66639]: No default Ryckaert-Bell. types (there are 160 of those). From what I could see in this mailing list, it seems the error comes from the choice of the atom types for the phosphate groups. I have tried several of them which seemed to make sense, but none of them allowed to remove all the errors. The end of the chain is something like: O | (...)--CH2--O--P--O--H | O (details of the whole molecule here: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO ) The problem is about the atom type of the -OH group at the end. Here are the entries from the .atp file which I thought were relevant: opls_445 30.97376 ; P in MeOPO3--, MeOPO3H2 opls_446 15.99940 ; O= in MeOPO3--, MeOPO3H2 opls_447 15.99940 ; OMe in MeOPO3--, MeOPO3H2 methyl phosphate opls_448 12.01100 ; C in MeOPO3--, MeOPO3H2 6-31+G* CHELPG opls_449 1.00800 ; H in MeOPO3--, MeOPO3H2 I chose opls_445 for the P, opls_446 for the 3 oxygens, and opls_449 for the hydrogen. Apparently, I got it wrong for the oxygen and the hydrogen of the OH group, at least. Unless the error actually comes from something else... So my question is the following: Have I done something wrong about the atom types? If so, does anyone know which atom type I should choose? The problem isn't necessarily the atom types themselves (which seem to be reasonable enough from the information provided), but rather that there are no default bonded parameters for these interactions. If you look into ffnonbonded.itp, the second column is entitled bond_type and thus refers to the names used by grompp when interpreting how atoms are connected. The actual bond, angle, and dihedral parameters are in ffbonded.itp, using these names. You would have to map out what the bond_type names are for each of these and find/derive new parameters for each of the interactions that are missing. -Justin Details of my rtp entry: [ CAP ] [ atoms ] P1 opls_445 1.539429 1 O1P opls_446 −0.818751 1 O2P opls_446 −0.899293 1 HO2P opls_449 0.429028 1 O3P opls_446 −0.895147 1 O1 opls_447 −0.772438 2 C1 opls_448 0.022084 3 HC11 opls_449 0.176920 3 HC12 opls_449 0.139342 3 C2 opls_159 0.146383 4 O2 opls_154 −0.883774 4 HO2 opls_155 0.527657 4 C opls_271 0.815849 5 O6 opls_271 −0.766517 5 O7 opls_272 −0.771422 5 C3 opls_158 0.142583 6 HC3 opls_140 0.107158 6 O3 opls_154 −0.817159 6 HO3 opls_155 0.471262 6 C4 opls_158 0.184473 7 HC4 opls_140 0.164192 7 O4 opls_154 −0.822792 7 HO4 opls_155 0.498509 7 C5 opls_448 0.038563 8 HC51 opls_449 0.143027 8 HC52 opls_449 0.135804 8 O5 opls_447 −0.730025 9 P2 opls_445 1.526672 10 O4P opls_446 −0.866625 10 O5P opls_446 −0.810148 10 HO5P opls_449 0.521464 10 O6P opls_446 −0.876311 10 [ bonds ] HO2P O2P O1P P1 O2P P2 O3P P1 P1 O1 O1 C1 C1 HC11 C1 HC12 C1 C2 C2 O2 O2 HO2 C2 C C O6 C O7 C2 C3 C3 O3 C3 HC3 O3 HO3 C3 C4 C4 HC4 C4 O4 O4 HO4 C4 C5 C5 HC51 C5 HC52 C5 O5 O5 P2 P2 O4P P2 O5P P2 O6P O5P HO5P Thank you very much in advance! Antoine -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field
Dear Justin, Many thanks for your response. I managed to reduce the number of errors by trying other atom types, by looking at what seemed most likely to be right from the ffnonbonded.itp and ffbonded.itp files. Unfortunately, I did not manage to find a combination that both made some sense, and allowed to remove the errors. So I guess these things need to be parametrized, as you said. Could you possibly let me know if there is a relatively easy and straightforward way to find these parameters? (I guess the answer is probably no, but it's always worth asking, I guess...) I also noticed that there is a option -zero in grompp which Sets parameters for bonded interactions without defaults to zero instead of generating an error. What does it mean exactly? Is it just taking the angles and distances inferred from the structure as the ones at equilibrium? Is it safe to use it? I am just a beginner with MD, and I just want to do a quick run to test something. I have no need for super high accuracy, and the run I want to try will be very small (maybe 1 or 2 ns, or something like that), and for a very large system (~80 000 atoms). Would that be unreasonable to use that -zero option (it is tempting, I must say...)? Thanks, Antoine On 26/04/12 12:53, Justin A. Lemkul wrote: On 4/26/12 7:45 AM, Delmotte, Antoine wrote: Dear Gromacs users, I am here requesting your help with regards to the editing of the OPLS-AA force field, and more specifically, the choice of the atom types. I have added an entry for the molecule CABP to the .rtp and .hdb files. I can run pdb2gmx, genbox and editconf without getting any error. However, when I run grompp, I receive the following errors: ERROR 1 [file 1RBO_Protein_chain_A.itp, line 15054]: No default Bond types ERROR 78 [file 1RBO_Protein_chain_M.itp, line 47276]: No default Angle types ERROR 82 [file 1RBO_Protein_chain_M.itp, line 66639]: No default Ryckaert-Bell. types (there are 160 of those). From what I could see in this mailing list, it seems the error comes from the choice of the atom types for the phosphate groups. I have tried several of them which seemed to make sense, but none of them allowed to remove all the errors. The end of the chain is something like: O | (...)--CH2--O--P--O--H | O (details of the whole molecule here: http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO http://www.rcsb.org/pdb/ligand/ligandsummary.do?hetId=CAPsid=1RBO ) The problem is about the atom type of the -OH group at the end. Here are the entries from the .atp file which I thought were relevant: opls_445 30.97376 ; P in MeOPO3--, MeOPO3H2 opls_446 15.99940 ; O= in MeOPO3--, MeOPO3H2 opls_447 15.99940 ; OMe in MeOPO3--, MeOPO3H2 methyl phosphate opls_448 12.01100 ; C in MeOPO3--, MeOPO3H2 6-31+G* CHELPG opls_449 1.00800 ; H in MeOPO3--, MeOPO3H2 I chose opls_445 for the P, opls_446 for the 3 oxygens, and opls_449 for the hydrogen. Apparently, I got it wrong for the oxygen and the hydrogen of the OH group, at least. Unless the error actually comes from something else... So my question is the following: Have I done something wrong about the atom types? If so, does anyone know which atom type I should choose? The problem isn't necessarily the atom types themselves (which seem to be reasonable enough from the information provided), but rather that there are no default bonded parameters for these interactions. If you look into ffnonbonded.itp, the second column is entitled bond_type and thus refers to the names used by grompp when interpreting how atoms are connected. The actual bond, angle, and dihedral parameters are in ffbonded.itp, using these names. You would have to map out what the bond_type names are for each of these and find/derive new parameters for each of the interactions that are missing. -Justin Details of my rtp entry: [ CAP ] [ atoms ] P1 opls_445 1.539429 1 O1P opls_446 −0.818751 1 O2P opls_446 −0.899293 1 HO2P opls_449 0.429028 1 O3P opls_446 −0.895147 1 O1 opls_447 −0.772438 2 C1 opls_448 0.022084 3 HC11 opls_449 0.176920 3 HC12 opls_449 0.139342 3 C2 opls_159 0.146383 4 O2 opls_154 −0.883774 4 HO2 opls_155 0.527657 4 C opls_271 0.815849 5 O6 opls_271 −0.766517 5 O7 opls_272 −0.771422 5 C3 opls_158 0.142583 6 HC3 opls_140 0.107158 6 O3 opls_154 −0.817159 6 HO3 opls_155 0.471262 6 C4 opls_158 0.184473 7 HC4 opls_140 0.164192 7 O4 opls_154 −0.822792 7 HO4 opls_155 0.498509 7 C5 opls_448 0.038563 8 HC51 opls_449 0.143027 8 HC52 opls_449 0.135804 8 O5 opls_447 −0.730025 9 P2 opls_445 1.526672 10 O4P opls_446 −0.866625 10 O5P opls_446 −0.810148 10 HO5P opls_449 0.521464 10 O6P opls_446 −0.876311 10 [ bonds ] HO2P O2P O1P P1 O2P P2 O3P P1 P1 O1 O1 C1 C1 HC11 C1 HC12 C1 C2 C2 O2 O2 HO2 C2 C C O6 C O7 C2 C3 C3 O3 C3 HC3 O3 HO3 C3 C4 C4 HC4 C4 O4 O4 HO4 C4 C5 C5 HC51 C5 HC52 C5 O5 O5 P2 P2 O4P P2 O5P P2 O6P O5P HO5P Thank you very much in advance! Antoine -- gmx-users mailing list
Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field
On 4/26/12 11:37 AM, Delmotte, Antoine wrote: Dear Justin, Many thanks for your response. I managed to reduce the number of errors by trying other atom types, by looking at what seemed most likely to be right from the ffnonbonded.itp and ffbonded.itp files. Unfortunately, I did not manage to find a combination that both made some sense, and allowed to remove the errors. So I guess these things need to be parametrized, as you said. Could you possibly let me know if there is a relatively easy and straightforward way to find these parameters? (I guess the answer is probably no, but it's always worth asking, I guess...) You can make a first effort by assigning parameters based on existing, similar, parameters. They may or may not exist. I also noticed that there is a option -zero in grompp which Sets parameters for bonded interactions without defaults to zero instead of generating an error. What does it mean exactly? Is it just taking the angles and distances inferred from the structure as the ones at equilibrium? Is it safe to use it? What it means is ignore the problem and simply assign the value of zero for equilibrium lengths, force constants, etc. I am just a beginner with MD, and I just want to do a quick run to test something. I have no need for super high accuracy, and the run I want to try will be very small (maybe 1 or 2 ns, or something like that), and for a very large system (~80 000 atoms). Would that be unreasonable to use that -zero option (it is tempting, I must say...)? I say that using -zero is a bad idea. It ignores the problem and whatever results you obtain would be questionable, at best. Parameterization of novel species is an advanced topic. Most people will spend several months developing good parameters for a new residue or molecule. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field
Thank you very much for your answer. This has been very helpful. I think I will follow your advice and try to find similar molecules to find the parameters. Could I just ask you if you know of a database where I could look for the opls parameters which have calculated for other molecules? Best regards, Antoine On 26/04/12 16:55, Justin A. Lemkul wrote: On 4/26/12 11:37 AM, Delmotte, Antoine wrote: Dear Justin, Many thanks for your response. I managed to reduce the number of errors by trying other atom types, by looking at what seemed most likely to be right from the ffnonbonded.itp and ffbonded.itp files. Unfortunately, I did not manage to find a combination that both made some sense, and allowed to remove the errors. So I guess these things need to be parametrized, as you said. Could you possibly let me know if there is a relatively easy and straightforward way to find these parameters? (I guess the answer is probably no, but it's always worth asking, I guess...) You can make a first effort by assigning parameters based on existing, similar, parameters. They may or may not exist. I also noticed that there is a option -zero in grompp which Sets parameters for bonded interactions without defaults to zero instead of generating an error. What does it mean exactly? Is it just taking the angles and distances inferred from the structure as the ones at equilibrium? Is it safe to use it? What it means is ignore the problem and simply assign the value of zero for equilibrium lengths, force constants, etc. I am just a beginner with MD, and I just want to do a quick run to test something. I have no need for super high accuracy, and the run I want to try will be very small (maybe 1 or 2 ns, or something like that), and for a very large system (~80 000 atoms). Would that be unreasonable to use that -zero option (it is tempting, I must say...)? I say that using -zero is a bad idea. It ignores the problem and whatever results you obtain would be questionable, at best. Parameterization of novel species is an advanced topic. Most people will spend several months developing good parameters for a new residue or molecule. -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
Re: [gmx-users] Atom types for phosphate group in OPLS-AA force field
On 4/26/12 12:15 PM, Delmotte, Antoine wrote: Thank you very much for your answer. This has been very helpful. I think I will follow your advice and try to find similar molecules to find the parameters. Could I just ask you if you know of a database where I could look for the opls parameters which have calculated for other molecules? There is a large database at http://virtualchemistry.org/index.php but I don't know if there will necessarily be anything similar to what you're looking for. -Justin Best regards, Antoine On 26/04/12 16:55, Justin A. Lemkul wrote: On 4/26/12 11:37 AM, Delmotte, Antoine wrote: Dear Justin, Many thanks for your response. I managed to reduce the number of errors by trying other atom types, by looking at what seemed most likely to be right from the ffnonbonded.itp and ffbonded.itp files. Unfortunately, I did not manage to find a combination that both made some sense, and allowed to remove the errors. So I guess these things need to be parametrized, as you said. Could you possibly let me know if there is a relatively easy and straightforward way to find these parameters? (I guess the answer is probably no, but it's always worth asking, I guess...) You can make a first effort by assigning parameters based on existing, similar, parameters. They may or may not exist. I also noticed that there is a option -zero in grompp which Sets parameters for bonded interactions without defaults to zero instead of generating an error. What does it mean exactly? Is it just taking the angles and distances inferred from the structure as the ones at equilibrium? Is it safe to use it? What it means is ignore the problem and simply assign the value of zero for equilibrium lengths, force constants, etc. I am just a beginner with MD, and I just want to do a quick run to test something. I have no need for super high accuracy, and the run I want to try will be very small (maybe 1 or 2 ns, or something like that), and for a very large system (~80 000 atoms). Would that be unreasonable to use that -zero option (it is tempting, I must say...)? I say that using -zero is a bad idea. It ignores the problem and whatever results you obtain would be questionable, at best. Parameterization of novel species is an advanced topic. Most people will spend several months developing good parameters for a new residue or molecule. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] atom types
Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ and QQ? Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Sorry to labour on this but: I don't quite understand what you mean when you say that nonbonded pair interactions are not Coulombic. Surely nonbonded charged atoms interact with each other, when close enough? (or by Nonbonded pair interactions do you explcitly mean 1-4,1-5, etc.) What are the 1-4 Coulombic interactions generated by, if not by gen_pairs =yes in my case? I have read this section of the manual loads and though I had a comprehensive understanding of it, but now I am confused again. Sure, there are nonbonded interactions for 1-4, 1-5, etc. But the purpose of [pairtype] generation is for LJ terms only. They are special 1-4 interactions between different atomtypes. Look at any force field for which [pairtypes] are listed - they have only C6 and C12 terms. Charges are not used for these calculations, but they are applied later during the MD using normal Coulombic equations and FudgeQQ. -Justin Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. -Justin Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- 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
Re: [gmx-users] atom types
On 02/08/11, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ and QQ? Does manual section 5.3.4 answer your question? Mark Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Sorry to labour on this but: I don't quite understand what you mean when you say that nonbonded pair interactions are not Coulombic. Surely nonbonded charged atoms interact with each other, when close enough? (or by Nonbonded pair interactions do you explcitly mean 1-4,1-5, etc.) What are the 1-4 Coulombic interactions generated by, if not by gen_pairs =yes in my case? I have read this section of the manual loads and though I had a comprehensive understanding of it, but now I am confused again. Sure, there are nonbonded interactions for 1-4, 1-5, etc. But the purpose of [pairtype] generation is for LJ terms only. They are special 1-4 interactions between different atomtypes. Look at any force field for which [pairtypes] are listed - they have only C6 and C12 terms. Charges are not used for these calculations, but they are applied later during the MD using normal Coulombic equations and FudgeQQ. -Justin Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. -Justin Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 3 yes 0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGE CH 24 0.3320 13.0190 73 C2 1 CGE C2 25 0. 14.0270 74 C2 1 CGE C2 25 0. 14.0270 75 C2 1 CGE C2 25 0. 14.0270 76 C2 1 CGE C2 26 0. 14.0270 77 C2 1 CGE C2 26 0. 14.0270 78 C2 1 CGE C2 26 0. 14.0270 79 C2 1 CGE C2 27 0. 14.0270 80 C2 1 CGE C2 27 0. 14.0270 81 C2 1 CGE C2 27 0. 14.0270 82 C2 1 CGE C2 28 0. 14.0270 83 CH 1 CGE CH 28 0. 13.0190 84 C3 1 CGE C3 29
Re: [gmx-users] atom types
Hi Mark Thanks for the reply. I am currently reading that section of the manual and, unless I am completely mistaken, it seems to vindicate what I am saying. Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [pairs] section of a molecule definition. In my [atom types] directive I have atomtype, charge mass, sigma and epsilon etc. All nonbonding parameters are then calculated according to the combination rule (in my case 3). 1-4 interactions are then calculated based on the information in [pairs] directive (all atoms are three bond away). I just have the atom indices of each pair in this directive therefore with gen_pairs = yes, the interaction parameters between each pair (which are 1-4) are calculated based on Fudge LJ and Fudge QQ (which are both 0.5 in my case). All of this in conjunction with nrexcl =3. Or am I completely wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? Many Thanks Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ and QQ? Does manual section 5.3.4 answer your question? Mark Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin Sorry to labour on this but: I don't quite understand what you mean when you say that nonbonded pair interactions are not Coulombic. Surely nonbonded charged atoms interact with each other, when close enough? (or by Nonbonded pair interactions do you explcitly mean 1-4,1-5, etc.) What are the 1-4 Coulombic interactions generated by, if not by gen_pairs =yes in my case? I have read this section of the manual loads and though I had a comprehensive understanding of it, but now I am confused again. Sure, there are nonbonded interactions for 1-4, 1-5, etc. But the purpose of [pairtype] generation is for LJ terms only. They are special 1-4 interactions between different atomtypes. Look at any force field for which [pairtypes] are listed - they have only C6 and C12 terms. Charges are not used for these calculations, but they are applied later during the MD using normal Coulombic equations and FudgeQQ. -Justin Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. -Justin Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype]
Re: [gmx-users] atom types
On 02/08/11, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi Mark Thanks for the reply. I am currently reading that section of the manual and, unless I am completely mistaken, it seems to vindicate what I am saying. Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [pairs] section of a molecule definition. In my [atom types] directive I have atomtype, charge mass, sigma and epsilon etc. All nonbonding parameters are then calculated according to the combination rule (in my case 3). 1-4 interactions are then calculated based on the information in [pairs] directive (all atoms are three bond away). I just have the atom indices of each pair in this directive therefore with gen_pairs = yes, the interaction parameters between each pair (which are 1-4) are calculated based on Fudge LJ and Fudge QQ (which are both 0.5 in my case). All of this in conjunction with nrexcl =3. That will generate parameters for the interactions listed in [pairs] that do not have corresponding [pairtypes]. FudgeLJ and [nonbond_params] are used in such generation, per other parts of 5.7. Or am I completely wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? If the contradiction you think exists is this one... On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ and QQ? ... then 5.3.4 indicates that the presence of a [pairs] directive will generate the 1,4 output fields. The parameters for that output are taken from [pairtypes]. If gen-pairs=yes then the parameters are generated, else some warning/error occurs. The example in 5.7.1 has some more explanation about the use of the fudge parameters. 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/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] atom types
Yes I think the example vindicates what I am saying as well. I suppose I the contradiction ( I'll call it the point of confusion) you refer to is perhaps when Justin (who is always more than helpful) said that Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. My sequence of 1-4 interaction generation should go like this I suppose: e.g. [pairs] 3 6 no parameters present therefore get from [pairtypes] directive. no [pairtypes] directive therefore get from [non_bonded parameters] directive as gen pairs = yes again no [non_bonded parameters] directive. Therefore generate 1,4 interaction parameters based on the normal sigma and epsilon values (comb rule 3) present in [atomtypes] directive, in accordance with fudge LJ and QQ. My point is, then in conclusion, that in this way surely the 1,4 electrostatic interactions are determined by the pair list and in my case gen_pairs = yes no? Many Thanks Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Mark Thanks for the reply. I am currently reading that section of the manual and, unless I am completely mistaken, it seems to vindicate what I am saying. Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [pairs] section of a molecule definition. In my [atom types] directive I have atomtype, charge mass, sigma and epsilon etc. All nonbonding parameters are then calculated according to the combination rule (in my case 3). 1-4 interactions are then calculated based on the information in [pairs] directive (all atoms are three bond away). I just have the atom indices of each pair in this directive therefore with gen_pairs = yes, the interaction parameters between each pair (which are 1-4) are calculated based on Fudge LJ and Fudge QQ (which are both 0.5 in my case). All of this in conjunction with nrexcl =3. That will generate parameters for the interactions listed in [pairs] that do not have corresponding [pairtypes]. FudgeLJ and [nonbond_params] are used in such generation, per other parts of 5.7. Or am I completely wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? If the contradiction you think exists is this one... On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ and QQ? ... then 5.3.4 indicates that the presence of a [pairs] directive will generate the 1,4 output fields. The parameters for that output are taken from [pairtypes]. If gen-pairs=yes then the parameters are generated, else some warning/error occurs. The example in 5.7.1 has some more explanation about the use of the fudge parameters. 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/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] atom types
Gavin Melaugh wrote: Yes I think the example vindicates what I am saying as well. I suppose I the contradiction ( I'll call it the point of confusion) you refer to is perhaps when Justin (who is always more than helpful) said that Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. Charges *are* irrelevant - the information is not used when generating pairs, which I thought was the original question. The charge information is used during MD, when the pair list tells mdrun which atoms interact in what way. Then you get Coul. 1-4 terms. Perhaps I missed your point, but this whole thread started as which charge is used to generate pairs? The answer is still none. My sequence of 1-4 interaction generation should go like this I suppose: e.g. [pairs] 3 6 no parameters present therefore get from [pairtypes] directive. no [pairtypes] directive therefore get from [non_bonded parameters] directive as gen pairs = yes again no [non_bonded parameters] directive. Therefore generate 1,4 interaction parameters based on the normal sigma and epsilon values (comb rule 3) present in [atomtypes] directive, in accordance with fudge LJ and QQ. My point is, then in conclusion, that in this way surely the 1,4 electrostatic interactions are determined by the pair list and in my case gen_pairs = yes no? Yes. -Justin Many Thanks Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Mark Thanks for the reply. I am currently reading that section of the manual and, unless I am completely mistaken, it seems to vindicate what I am saying. Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [pairs] section of a molecule definition. In my [atom types] directive I have atomtype, charge mass, sigma and epsilon etc. All nonbonding parameters are then calculated according to the combination rule (in my case 3). 1-4 interactions are then calculated based on the information in [pairs] directive (all atoms are three bond away). I just have the atom indices of each pair in this directive therefore with gen_pairs = yes, the interaction parameters between each pair (which are 1-4) are calculated based on Fudge LJ and Fudge QQ (which are both 0.5 in my case). All of this in conjunction with nrexcl =3. That will generate parameters for the interactions listed in [pairs] that do not have corresponding [pairtypes]. FudgeLJ and [nonbond_params] are used in such generation, per other parts of 5.7. Or am I completely wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? If the contradiction you think exists is this one... On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ and QQ? ... then 5.3.4 indicates that the presence of a [pairs] directive will generate the 1,4 output fields. The parameters for that output are taken from [pairtypes]. If gen-pairs=yes then the parameters are generated, else some warning/error occurs. The example in 5.7.1 has some more explanation about the use of the fudge parameters. Mark -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] atom types
Hi Justin I see that we may have got our wires crossed from the off. Consider the [pairs] directive, which determines which atoms interact in a 1,4 manner. Consider two atoms listed the [pairs] directive. From the point of the Coulombic interaction between these two atoms I suppose my original question should have been: Does mdrun, when calculating the Coulombic potential between these two atoms, use the charges assigned to the atoms in the [atomtypes] directive or [atoms] directive ? Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Yes I think the example vindicates what I am saying as well. I suppose I the contradiction ( I'll call it the point of confusion) you refer to is perhaps when Justin (who is always more than helpful) said that Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. Charges *are* irrelevant - the information is not used when generating pairs, which I thought was the original question. The charge information is used during MD, when the pair list tells mdrun which atoms interact in what way. Then you get Coul. 1-4 terms. Perhaps I missed your point, but this whole thread started as which charge is used to generate pairs? The answer is still none. My sequence of 1-4 interaction generation should go like this I suppose: e.g. [pairs] 3 6 no parameters present therefore get from [pairtypes] directive. no [pairtypes] directive therefore get from [non_bonded parameters] directive as gen pairs = yes again no [non_bonded parameters] directive. Therefore generate 1,4 interaction parameters based on the normal sigma and epsilon values (comb rule 3) present in [atomtypes] directive, in accordance with fudge LJ and QQ. My point is, then in conclusion, that in this way surely the 1,4 electrostatic interactions are determined by the pair list and in my case gen_pairs = yes no? Yes. -Justin Many Thanks Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Mark Thanks for the reply. I am currently reading that section of the manual and, unless I am completely mistaken, it seems to vindicate what I am saying. Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [pairs] section of a molecule definition. In my [atom types] directive I have atomtype, charge mass, sigma and epsilon etc. All nonbonding parameters are then calculated according to the combination rule (in my case 3). 1-4 interactions are then calculated based on the information in [pairs] directive (all atoms are three bond away). I just have the atom indices of each pair in this directive therefore with gen_pairs = yes, the interaction parameters between each pair (which are 1-4) are calculated based on Fudge LJ and Fudge QQ (which are both 0.5 in my case). All of this in conjunction with nrexcl =3. That will generate parameters for the interactions listed in [pairs] that do not have corresponding [pairtypes]. FudgeLJ and [nonbond_params] are used in such generation, per other parts of 5.7. Or am I completely wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? If the contradiction you think exists is this one... On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ and QQ? ... then 5.3.4 indicates that the presence of a [pairs] directive will generate the 1,4 output fields. The parameters for that output are taken from [pairtypes]. If gen-pairs=yes then the parameters are generated, else some warning/error occurs. The example in 5.7.1 has some more explanation about the use of the fudge parameters. 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/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] atom types
On 02/08/11, Gavin Melaugh gmelaug...@qub.ac.uk wrote: Hi Justin I see that we may have got our wires crossed from the off. Consider the [pairs] directive, which determines which atoms interact in a 1,4 manner. Consider two atoms listed the [pairs] directive. From the point of the Coulombic interaction between these two atoms I suppose my original question should have been: Does mdrun, when calculating the Coulombic potential between these two atoms, use the charges assigned to the atoms in the [atomtypes] directive or [atoms] directive ? The charges from [atoms] are used. The charges in [atomtypes] are never used in any forcefield currently used with GROMACS. It might not be possible for grompp to ever use them, but I'd have to check the code for that. Mark Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Yes I think the example vindicates what I am saying as well. I suppose I the contradiction ( I'll call it the point of confusion) you refer to is perhaps when Justin (who is always more than helpful) said that Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. Charges *are* irrelevant - the information is not used when generating pairs, which I thought was the original question. The charge information is used during MD, when the pair list tells mdrun which atoms interact in what way. Then you get Coul. 1-4 terms. Perhaps I missed your point, but this whole thread started as which charge is used to generate pairs? The answer is still none. My sequence of 1-4 interaction generation should go like this I suppose: e.g. [pairs] 3 6 no parameters present therefore get from [pairtypes] directive. no [pairtypes] directive therefore get from [non_bonded parameters] directive as gen pairs = yes again no [non_bonded parameters] directive. Therefore generate 1,4 interaction parameters based on the normal sigma and epsilon values (comb rule 3) present in [atomtypes] directive, in accordance with fudge LJ and QQ. My point is, then in conclusion, that in this way surely the 1,4 electrostatic interactions are determined by the pair list and in my case gen_pairs = yes no? Yes. -Justin Many Thanks Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Mark Thanks for the reply. I am currently reading that section of the manual and, unless I am completely mistaken, it seems to vindicate what I am saying. Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [pairs] section of a molecule definition. In my [atom types] directive I have atomtype, charge mass, sigma and epsilon etc. All nonbonding parameters are then calculated according to the combination rule (in my case 3). 1-4 interactions are then calculated based on the information in [pairs] directive (all atoms are three bond away). I just have the atom indices of each pair in this directive therefore with gen_pairs = yes, the interaction parameters between each pair (which are 1-4) are calculated based on Fudge LJ and Fudge QQ (which are both 0.5 in my case). All of this in conjunction with nrexcl =3. That will generate parameters for the interactions listed in [pairs] that do not have corresponding [pairtypes]. FudgeLJ and [nonbond_params] are used in such generation, per other parts of 5.7. Or am I completely wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? If the contradiction you think exists is this one... On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ and QQ? ... then 5.3.4 indicates that the presence of a [pairs] directive will generate the 1,4 output fields. The parameters for that output are taken from [pairtypes]. If gen-pairs=yes then the parameters are generated, else some warning/error occurs. The example in 5.7.1 has some more explanation about the use of the fudge parameters. Mark -- gmx-users mailing list gmx-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
Re: [gmx-users] atom types
I hope this doesn't come across as stupid, or worse insolent. But what is the point in stating the charges in the atom type section then ? Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin I see that we may have got our wires crossed from the off. Consider the [pairs] directive, which determines which atoms interact in a 1,4 manner. Consider two atoms listed the [pairs] directive. From the point of the Coulombic interaction between these two atoms I suppose my original question should have been: Does mdrun, when calculating the Coulombic potential between these two atoms, use the charges assigned to the atoms in the [atomtypes] directive or [atoms] directive ? The charges from [atoms] are used. The charges in [atomtypes] are never used in any forcefield currently used with GROMACS. It might not be possible for grompp to ever use them, but I'd have to check the code for that. Mark Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Yes I think the example vindicates what I am saying as well. I suppose I the contradiction ( I'll call it the point of confusion) you refer to is perhaps when Justin (who is always more than helpful) said that Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. Charges *are* irrelevant - the information is not used when generating pairs, which I thought was the original question. The charge information is used during MD, when the pair list tells mdrun which atoms interact in what way. Then you get Coul. 1-4 terms. Perhaps I missed your point, but this whole thread started as which charge is used to generate pairs? The answer is still none. My sequence of 1-4 interaction generation should go like this I suppose: e.g. [pairs] 3 6 no parameters present therefore get from [pairtypes] directive. no [pairtypes] directive therefore get from [non_bonded parameters] directive as gen pairs = yes again no [non_bonded parameters] directive. Therefore generate 1,4 interaction parameters based on the normal sigma and epsilon values (comb rule 3) present in [atomtypes] directive, in accordance with fudge LJ and QQ. My point is, then in conclusion, that in this way surely the 1,4 electrostatic interactions are determined by the pair list and in my case gen_pairs = yes no? Yes. -Justin Many Thanks Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Mark Thanks for the reply. I am currently reading that section of the manual and, unless I am completely mistaken, it seems to vindicate what I am saying. Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [pairs] section of a molecule definition. In my [atom types] directive I have atomtype, charge mass, sigma and epsilon etc. All nonbonding parameters are then calculated according to the combination rule (in my case 3). 1-4 interactions are then calculated based on the information in [pairs] directive (all atoms are three bond away). I just have the atom indices of each pair in this directive therefore with gen_pairs = yes, the interaction parameters between each pair (which are 1-4) are calculated based on Fudge LJ and Fudge QQ (which are both 0.5 in my case). All of this in conjunction with nrexcl =3. That will generate parameters for the interactions listed in [pairs] that do not have corresponding [pairtypes]. FudgeLJ and [nonbond_params] are used in such generation, per other parts of 5.7. Or am I completely wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? If the contradiction you think exists is this one... On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and 1,4 Coulomb according to fudge LJ and QQ? ... then 5.3.4 indicates that the presence of a [pairs] directive will generate the 1,4 output fields. The parameters for that output are taken from [pairtypes]. If gen-pairs=yes then the parameters are generated, else some warning/error occurs. The example in 5.7.1 has some more explanation about the use of the fudge parameters. Mark -- gmx-users mailing listgmx-users@gromacs.org
Re: [gmx-users] atom types
Gavin Melaugh wrote: I hope this doesn't come across as stupid, or worse insolent. But what is the point in stating the charges in the atom type section then ? They're probably a holdover from some earlier Gromacs version (an ancient one) that used those charges somehow, or they were listed there as some grand idea to have a more universal, streamlined topology builder that could use generic charges. Just a guess. They stayed there because it's far easier to just ignore the unnecessary information than the re-write the code and those files such that the lines are read properly with one less field. The charges can be useful for starting parameterization; they are based on common functional groups that may not be far off from the correct values in many cases. -Justin Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin I see that we may have got our wires crossed from the off. Consider the [pairs] directive, which determines which atoms interact in a 1,4 manner. Consider two atoms listed the [pairs] directive. From the point of the Coulombic interaction between these two atoms I suppose my original question should have been: Does mdrun, when calculating the Coulombic potential between these two atoms, use the charges assigned to the atoms in the [atomtypes] directive or [atoms] directive ? The charges from [atoms] are used. The charges in [atomtypes] are never used in any forcefield currently used with GROMACS. It might not be possible for grompp to ever use them, but I'd have to check the code for that. Mark Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Yes I think the example vindicates what I am saying as well. I suppose I the contradiction ( I'll call it the point of confusion) you refer to is perhaps when Justin (who is always more than helpful) said that Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. Charges *are* irrelevant - the information is not used when generating pairs, which I thought was the original question. The charge information is used during MD, when the pair list tells mdrun which atoms interact in what way. Then you get Coul. 1-4 terms. Perhaps I missed your point, but this whole thread started as which charge is used to generate pairs? The answer is still none. My sequence of 1-4 interaction generation should go like this I suppose: e.g. [pairs] 3 6 no parameters present therefore get from [pairtypes] directive. no [pairtypes] directive therefore get from [non_bonded parameters] directive as gen pairs = yes again no [non_bonded parameters] directive. Therefore generate 1,4 interaction parameters based on the normal sigma and epsilon values (comb rule 3) present in [atomtypes] directive, in accordance with fudge LJ and QQ. My point is, then in conclusion, that in this way surely the 1,4 electrostatic interactions are determined by the pair list and in my case gen_pairs = yes no? Yes. -Justin Many Thanks Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Mark Thanks for the reply. I am currently reading that section of the manual and, unless I am completely mistaken, it seems to vindicate what I am saying. Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [pairs] section of a molecule definition. In my [atom types] directive I have atomtype, charge mass, sigma and epsilon etc. All nonbonding parameters are then calculated according to the combination rule (in my case 3). 1-4 interactions are then calculated based on the information in [pairs] directive (all atoms are three bond away). I just have the atom indices of each pair in this directive therefore with gen_pairs = yes, the interaction parameters between each pair (which are 1-4) are calculated based on Fudge LJ and Fudge QQ (which are both 0.5 in my case). All of this in conjunction with nrexcl =3. That will generate parameters for the interactions listed in [pairs] that do not have corresponding [pairtypes]. FudgeLJ and [nonbond_params] are used in such generation, per other parts of 5.7. Or am I completely wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? If the contradiction you think exists is this one... On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you but If I don't include a [pairs] directive in the topology file (with gen_pairs =yes), then there are no 1-4 LJ nor 1-4 Coulombic energies written in the log file. When I include the [pair s] directive then both types of interaction are written to the log file. Therefore does gen_pairs= yes + [pairs] directive generate 1,4 LJ and
Re: [gmx-users] atom types
On 02/08/11, Gavin Melaugh gmelaug...@qub.ac.uk wrote: I hope this doesn't come across as stupid, or worse insolent. But what is the point in stating the charges in the atom type section then ? It would make sense for a force field that had a fixed charge for some/all atom types. If any such force fields exist, they don't get used for biomolecular MD. I don't know if such a force field can be implemented in GROMACS (per my earlier comment about checking the code). In some cases, grompp does a bunch of fancy footwork to try to infer the format of the content of the input lines. It's possible it can recognize that a charge field is missing and perhaps the charge gets read from [atomtypes] - but that is just not useful for biomolecular MD. Another possibility is that the file formats serve other purposes (possibly in the distant past). Mark Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin I see that we may have got our wires crossed from the off. Consider the [pairs] directive, which determines which atoms interact in a 1,4 manner. Consider two atoms listed the [pairs] directive. From the point of the Coulombic interaction between these two atoms I suppose my original question should have been: Does mdrun, when calculating the Coulombic potential between these two atoms, use the charges assigned to the atoms in the [atomtypes] directive or [atoms] directive ? The charges from [atoms] are used. The charges in [atomtypes] are never used in any forcefield currently used with GROMACS. It might not be possible for grompp to ever use them, but I'd have to check the code for that. Mark Cheers Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Yes I think the example vindicates what I am saying as well. I suppose I the contradiction ( I'll call it the point of confusion) you refer to is perhaps when Justin (who is always more than helpful) said that Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. Charges *are* irrelevant - the information is not used when generating pairs, which I thought was the original question. The charge information is used during MD, when the pair list tells mdrun which atoms interact in what way. Then you get Coul. 1-4 terms. Perhaps I missed your point, but this whole thread started as which charge is used to generate pairs? The answer is still none. My sequence of 1-4 interaction generation should go like this I suppose: e.g. [pairs] 3 6 no parameters present therefore get from [pairtypes] directive. no [pairtypes] directive therefore get from [non_bonded parameters] directive as gen pairs = yes again no [non_bonded parameters] directive. Therefore generate 1,4 interaction parameters based on the normal sigma and epsilon values (comb rule 3) present in [atomtypes] directive, in accordance with fudge LJ and QQ. My point is, then in conclusion, that in this way surely the 1,4 electrostatic interactions are determined by the pair list and in my case gen_pairs = yes no? Yes. -Justin Many Thanks Gavin Mark Abraham wrote: On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Mark Thanks for the reply. I am currently reading that section of the manual and, unless I am completely mistaken, it seems to vindicate what I am saying. Extra Lennard-Jones and electrostatic interactions between pairs of atoms in a molecule can be added in the [pairs] section of a molecule definition. In my [atom types] directive I have atomtype, charge mass, sigma and epsilon etc. All nonbonding parameters are then calculated according to the combination rule (in my case 3). 1-4 interactions are then calculated based on the information in [pairs] directive (all atoms are three bond away). I just have the atom indices of each pair in this directive therefore with gen_pairs = yes, the interaction parameters between each pair (which are 1-4) are calculated based on Fudge LJ and Fudge QQ (which are both 0.5 in my case). All of this in conjunction with nrexcl =3. That will generate parameters for the interactions listed in [pairs] that do not have corresponding [pairtypes]. FudgeLJ and [nonbond_params] are used in such generation, per other parts of 5.7. Or am I completely wrong? In my set up then, are 1-4 Coulombic interactions determined by the pair list and fudge QQ? If the contradiction you think exists is this one... On 02/08/11, *Gavin Melaugh * gmelaug...@qub.ac.uk wrote: Hi Justin Again thanks for the reply. I am not disagreeing with you
[gmx-users] atom types
Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- 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] atom types
Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] atom types
Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- 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] atom types
Gavin Melaugh wrote: Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. -Justin Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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
Re: [gmx-users] atom types
Hi Justin Sorry to labour on this but: I don't quite understand what you mean when you say that nonbonded pair interactions are not Coulombic. Surely nonbonded charged atoms interact with each other, when close enough? (or by Nonbonded pair interactions do you explcitly mean 1-4,1-5, etc.) What are the 1-4 Coulombic interactions generated by, if not by gen_pairs =yes in my case? I have read this section of the manual loads and though I had a comprehensive understanding of it, but now I am confused again. Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. -Justin Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- 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] atom types
Gavin Melaugh wrote: Hi Justin Sorry to labour on this but: I don't quite understand what you mean when you say that nonbonded pair interactions are not Coulombic. Surely nonbonded charged atoms interact with each other, when close enough? (or by Nonbonded pair interactions do you explcitly mean 1-4,1-5, etc.) What are the 1-4 Coulombic interactions generated by, if not by gen_pairs =yes in my case? I have read this section of the manual loads and though I had a comprehensive understanding of it, but now I am confused again. Sure, there are nonbonded interactions for 1-4, 1-5, etc. But the purpose of [pairtype] generation is for LJ terms only. They are special 1-4 interactions between different atomtypes. Look at any force field for which [pairtypes] are listed - they have only C6 and C12 terms. Charges are not used for these calculations, but they are applied later during the MD using normal Coulombic equations and FudgeQQ. -Justin Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi Justin I have checked the tpr file. Now it seems to assign the the two type of CHs as the same atom type, but at the same time with the specified charge from the [atoms] directive, as I expected. Concerning 1-4 interactions and gen_pairs =yes, my concern is this; from the pair list and using gen_pairs = yes, does grompp then take the 1-4 coulombic interaction for CH from the [atomtypes] directive (as the meaning of gen_pairs =yes)? Or does it assign the charge based on the atom index in the pair list? Charges are irrelevant for generation of pair interactions. Nonbonded pair interactions are LJ, not Coulombic. You will certainly have 1-4 Coulombic interactions, but they are not generated by gen_pairs. See manual section 5.3.4. -Justin Many Thanks Gavin Justin A. Lemkul wrote: Gavin Melaugh wrote: Hi all A very quick question. I have an atom-type labelled CH in the atom-types with a particular charge, and in the atom list I assign some of these specific atoms with zero charge as below. When I generate 1,4 interactions using gen_pairs =yes, what charge for the CH type does it use? Does gromacs assign the CH with the different charge as a new atom type. Charges set in [atomtypes] are not used. The zero charge is assigned. Verify this by using gmxdump on your .tpr file. -Justin ;Parameter level [defaults] ; nbfunccomb-rule gen-pairsfudgeLJ fudgeQQ 1 3 yes0.5 0.5 [atomtypes] ;type mass charge ptype sigma(nm) epsilon(kjmol-1) CB 12.011000 0.00 A 0.355000 0.292880 CA 12.011000 -0.115000 A 0.355000 0.292880 HC 1.008000 0.115000 A 0.242000 0.125520 CU 13.019000 0.265000 A 0.35 0.334720 NU 14.007000 -0.597000 A 0.325000 0.711280 CH 13.019000 0.332000 A 0.385000 0.334720 C3 15.035000 0.00 A 0.391000 0.669440 C2 14.027000 0.00 A 0.390500 0.493712 ;Molecular level [moleculetype] ; name nrexcl isotridecylcage 3 [atoms] . 72 CH 1 CGECH 24 0.3320 13.0190 73 C2 1 CGEC2 25 0. 14.0270 74 C2 1 CGEC2 25 0. 14.0270 75 C2 1 CGEC2 25 0. 14.0270 76 C2 1 CGEC2 26 0. 14.0270 77 C2 1 CGEC2 26 0. 14.0270 78 C2 1 CGEC2 26 0. 14.0270 79 C2 1 CGEC2 27 0. 14.0270 80 C2 1 CGEC2 27 0. 14.0270 81 C2 1 CGEC2 27 0. 14.0270 82 C2 1 CGEC2 28 0. 14.0270 83 CH 1 CGECH 28 0. 13.0190 84 C3 1 CGEC3 29 0. 15.0350 Many Thanks Gavin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Atom types of OPLS-AA
Dear gmx users, I want to study polyamide using OPLS-AA force field. But for the residues, -CH2-C(=O)-NH-CH2, I can not find suitable atom types for C, H, atoms on both sides. I wonder whether OPLS-AA can model this kind of polymers. Could you give me the answer? If it is, what are they? Thank you for attention! Best regards, Chaofu Wu _ 约会说不清地方？来试试微软地图最新msn互动功能！ http://ditu.live.com/?form=TLswm=1___ 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
[gmx-users] atom types @ bonded parameters
New to the list, aimed at installing gromacs on Linux Debian amd64 dual-core-opterons for parallel execution, I would appreciate indications where (not having yet installed gromacs) to find: ---Atom types list. ---Bonded parameters list. ---Any tool to generate new bonded parameters. I am well equipped of QM suites and have also some experience with classical MD. My problem was always lack of bonded parameters and atom types that I need for my studies. Thanks francesco pietra (This is a project of mine of long date, and I also had exchange of emails with the Debian gromacs maintainer; though, it is only now that I have the time to try to start). Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/ ___ 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] atom types @ bonded parameters
Francesco Pietra wrote: New to the list, aimed at installing gromacs on Linux Debian amd64 dual-core-opterons for parallel execution, I would appreciate indications where (not having yet installed gromacs) to find: ---Atom types list. ---Bonded parameters list. ---Any tool to generate new bonded parameters. share/gromacs/top I am well equipped of QM suites and have also some experience with classical MD. My problem was always lack of bonded parameters and atom types that I need for my studies. If you kow your QM a frequency calculation of your molecule should give you force constants and optimization the equilibrium distances and angles. only problem is torsion parameters. for these you have to read the appropriate force field papers. Thanks francesco pietra (This is a project of mine of long date, and I also had exchange of emails with the Debian gromacs maintainer; though, it is only now that I have the time to try to start). Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/ ___ 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
Re: [gmx-users] atom types @ bonded parameters
Thanks. The molecules have no repetitive units, though they have recurring moieties, such as five-membered to nine-membered saturated heterocycles, variously substituted. Is it safe to carry out the frequency task on each type of recurring moiety? I understand that without seeing it is difficult to judge, though my concept should be clear: evaluating the bonded parameters from sections of the actual molecule. With my molecules of 90 to 450 atoms, a QM geometry optimization/frequence calculation would be too time consuming at DFT theory, if a reliable functional and basis set is choose. Thanks francesco --- David van der Spoel [EMAIL PROTECTED] wrote: Francesco Pietra wrote: New to the list, aimed at installing gromacs on Linux Debian amd64 dual-core-opterons for parallel execution, I would appreciate indications where (not having yet installed gromacs) to find: ---Atom types list. ---Bonded parameters list. ---Any tool to generate new bonded parameters. share/gromacs/top I am well equipped of QM suites and have also some experience with classical MD. My problem was always lack of bonded parameters and atom types that I need for my studies. If you kow your QM a frequency calculation of your molecule should give you force constants and optimization the equilibrium distances and angles. only problem is torsion parameters. for these you have to read the appropriate force field papers. Thanks francesco pietra (This is a project of mine of long date, and I also had exchange of emails with the Debian gromacs maintainer; though, it is only now that I have the time to try to start). Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/ ___ 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 Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos more. http://mobile.yahoo.com/go?refer=1GNXIC ___ 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] atom types @ bonded parameters
Francesco Pietra wrote: Thanks. The molecules have no repetitive units, though they have recurring moieties, such as five-membered to nine-membered saturated heterocycles, variously substituted. Is it safe to carry out the frequency task on each type of recurring moiety? I understand that without seeing it is difficult to judge, though my concept should be clear: evaluating the bonded parameters from sections of the actual molecule. yes, this is how all biomolecular force fields are made. you might want to check up structure databases, there probably are crystal structures for the compounds. your biggest problem will be the nonbonded parameters however... you probably want to check out recent papers from the amber and/or opls people. you may also want to look up the antechamber program which generates force fields for arbitrary (well, almost) molecules. With my molecules of 90 to 450 atoms, a QM geometry optimization/frequence calculation would be too time consuming at DFT theory, if a reliable functional and basis set is choose. obviously. Thanks francesco -- 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
[gmx-users] atom types in share/gromacs/top/edissoc.dat
Dear GROMACS list members, What atom types are listed in the file share/gromacs/top/edissoc.dat and where can i find their description? Dmitry Egorov. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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] atom types in share/gromacs/top/edissoc.dat
egorov wrote: Dear GROMACS list members, What atom types are listed in the file share/gromacs/top/edissoc.dat and where can i find their description? Dmitry Egorov. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 These are used when grompp automatically convert a harmonic potential to a Morse type potential. The atomtypes correspond to old gromos force fields, the energies are probably from the Handbook of chemistry and physics. -- 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 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
