Re: [gmx-users] changing atom types versus adding dihedrals to atom types
Hmm, I will have to do some more controls then, but I prob dont have time to do them till after quals this fall... You mention Hartree-Fock methods, does this mean that you disfavor DFT for some reason for this purpose? On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote: Can you give some examples of how these verifications are different for different force fields? It doesnt seem like verifying takes that much time, but a theorist prof in my department told me not to worry as long as my system doesnt blow up... IMHO simply not blowing up tells you nothing. I can show you a dozen simulations that don't blow up that have terrible small molecule topologies that produce bad results. Parametrization methods and validation procedures are defined in the literature and one could easily fill a book chapter (or more) on such topics, so I will not go into it in an email. You may have to go back several years (or even decades) in the literature to get the full story. And what do you mean thourough parametrization? Most people hope for a simple, one-shot step they can take to parametrize a small molecule. There are numerous black box methods out there, some good and some bad. I advise people to be thorough in terms of what the force field requires and what their chemical knowledge tells them. For instance, for water interactions in CHARMM, HF/6-31G* works well for most compounds, unless sulfur is involved, in which case we need to do a more expensive MP2/6-31G* calculation. You can get an OK result for everything with HF, but it's not sufficiently accurate in all cases. I parametrized flavin mononucleotide using amber99sb-ildn, I used existing atomtypes in the force field, but I added partial atomic charges based on a decent DFT calculation in orca, and I had to add 2 distance restraints on the delta negatively charged phosphate oxygens to keep them from crashing into the delta positive hydrogen on the same phosphate. Is that thorough in your opinion? How does it compare with the results of running the molecule through antechamber? Usually GAFF gives a reasonable topology with minimal adjustment necessary. That's one of the benefits of Amber; there are very well-defined protocols and a robust general force field for the parametrization. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] changing atom types versus adding dihedrals to atom types
Sulpher is important, but it is in the apoprotein, not the parametrized prosthetic group On Thu, Sep 19, 2013 at 6:51 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: Hmm, I will have to do some more controls then, but I prob dont have time to do them till after quals this fall... You mention Hartree-Fock methods, does this mean that you disfavor DFT for some reason for this purpose? On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote: Can you give some examples of how these verifications are different for different force fields? It doesnt seem like verifying takes that much time, but a theorist prof in my department told me not to worry as long as my system doesnt blow up... IMHO simply not blowing up tells you nothing. I can show you a dozen simulations that don't blow up that have terrible small molecule topologies that produce bad results. Parametrization methods and validation procedures are defined in the literature and one could easily fill a book chapter (or more) on such topics, so I will not go into it in an email. You may have to go back several years (or even decades) in the literature to get the full story. And what do you mean thourough parametrization? Most people hope for a simple, one-shot step they can take to parametrize a small molecule. There are numerous black box methods out there, some good and some bad. I advise people to be thorough in terms of what the force field requires and what their chemical knowledge tells them. For instance, for water interactions in CHARMM, HF/6-31G* works well for most compounds, unless sulfur is involved, in which case we need to do a more expensive MP2/6-31G* calculation. You can get an OK result for everything with HF, but it's not sufficiently accurate in all cases. I parametrized flavin mononucleotide using amber99sb-ildn, I used existing atomtypes in the force field, but I added partial atomic charges based on a decent DFT calculation in orca, and I had to add 2 distance restraints on the delta negatively charged phosphate oxygens to keep them from crashing into the delta positive hydrogen on the same phosphate. Is that thorough in your opinion? How does it compare with the results of running the molecule through antechamber? Usually GAFF gives a reasonable topology with minimal adjustment necessary. That's one of the benefits of Amber; there are very well-defined protocols and a robust general force field for the parametrization. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] changing atom types versus adding dihedrals to atom types
On 9/19/13 9:51 PM, Rafael I. Silverman y de la Vega wrote: Sulpher is important, but it is in the apoprotein, not the parametrized prosthetic group I only mentioned this as one example where user input and intuition is useful, not necessarily to directly comment on anything you are doing. -Justin On Thu, Sep 19, 2013 at 6:51 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: Hmm, I will have to do some more controls then, but I prob dont have time to do them till after quals this fall... You mention Hartree-Fock methods, does this mean that you disfavor DFT for some reason for this purpose? On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote: Can you give some examples of how these verifications are different for different force fields? It doesnt seem like verifying takes that much time, but a theorist prof in my department told me not to worry as long as my system doesnt blow up... IMHO simply not blowing up tells you nothing. I can show you a dozen simulations that don't blow up that have terrible small molecule topologies that produce bad results. Parametrization methods and validation procedures are defined in the literature and one could easily fill a book chapter (or more) on such topics, so I will not go into it in an email. You may have to go back several years (or even decades) in the literature to get the full story. And what do you mean thourough parametrization? Most people hope for a simple, one-shot step they can take to parametrize a small molecule. There are numerous black box methods out there, some good and some bad. I advise people to be thorough in terms of what the force field requires and what their chemical knowledge tells them. For instance, for water interactions in CHARMM, HF/6-31G* works well for most compounds, unless sulfur is involved, in which case we need to do a more expensive MP2/6-31G* calculation. You can get an OK result for everything with HF, but it's not sufficiently accurate in all cases. I parametrized flavin mononucleotide using amber99sb-ildn, I used existing atomtypes in the force field, but I added partial atomic charges based on a decent DFT calculation in orca, and I had to add 2 distance restraints on the delta negatively charged phosphate oxygens to keep them from crashing into the delta positive hydrogen on the same phosphate. Is that thorough in your opinion? How does it compare with the results of running the molecule through antechamber? Usually GAFF gives a reasonable topology with minimal adjustment necessary. That's one of the benefits of Amber; there are very well-defined protocols and a robust general force field for the parametrization. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu| (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] changing atom types versus adding dihedrals to atom types
On 9/19/13 9:51 PM, Rafael I. Silverman y de la Vega wrote: Hmm, I will have to do some more controls then, but I prob dont have time to do them till after quals this fall... You mention Hartree-Fock methods, does this mean that you disfavor DFT for some reason for this purpose? For CHARMM, we use ab initio approaches that have been well documented in the literature. The molecules are all small enough that all the calculations take a couple hours or less. -Justin On Tue, Sep 17, 2013 at 5:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote: Can you give some examples of how these verifications are different for different force fields? It doesnt seem like verifying takes that much time, but a theorist prof in my department told me not to worry as long as my system doesnt blow up... IMHO simply not blowing up tells you nothing. I can show you a dozen simulations that don't blow up that have terrible small molecule topologies that produce bad results. Parametrization methods and validation procedures are defined in the literature and one could easily fill a book chapter (or more) on such topics, so I will not go into it in an email. You may have to go back several years (or even decades) in the literature to get the full story. And what do you mean thourough parametrization? Most people hope for a simple, one-shot step they can take to parametrize a small molecule. There are numerous black box methods out there, some good and some bad. I advise people to be thorough in terms of what the force field requires and what their chemical knowledge tells them. For instance, for water interactions in CHARMM, HF/6-31G* works well for most compounds, unless sulfur is involved, in which case we need to do a more expensive MP2/6-31G* calculation. You can get an OK result for everything with HF, but it's not sufficiently accurate in all cases. I parametrized flavin mononucleotide using amber99sb-ildn, I used existing atomtypes in the force field, but I added partial atomic charges based on a decent DFT calculation in orca, and I had to add 2 distance restraints on the delta negatively charged phosphate oxygens to keep them from crashing into the delta positive hydrogen on the same phosphate. Is that thorough in your opinion? How does it compare with the results of running the molecule through antechamber? Usually GAFF gives a reasonable topology with minimal adjustment necessary. That's one of the benefits of Amber; there are very well-defined protocols and a robust general force field for the parametrization. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] changing atom types versus adding dihedrals to atom types
Can you give some examples of how these verifications are different for different force fields? It doesnt seem like verifying takes that much time, but a theorist prof in my department told me not to worry as long as my system doesnt blow up... And what do you mean thourough parametrization? I parametrized flavin mononucleotide using amber99sb-ildn, I used existing atomtypes in the force field, but I added partial atomic charges based on a decent DFT calculation in orca, and I had to add 2 distance restraints on the delta negatively charged phosphate oxygens to keep them from crashing into the delta positive hydrogen on the same phosphate. Is that thorough in your opinion? Thanks On Thu, Sep 12, 2013 at 7:32 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/12/13 7:04 PM, Rafael I. Silverman y de la Vega wrote: I see, when you say thorough parametrization and validation, what do you mean? How does one validate the system, calculate free energy in solution and compare it to tabulated data? The target data depend on the force field for which parameters are being developed. Matching QM geometries, water interaction energies and distances, free energies of solvation, crystal structures, liquid properties, etc. are all useful depending on the underlying force field and how it was derived. For bonded parameters, matching QM energy scans and/or vibrational properties are common. -Justin On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote: Hi all, in another thread it was recommended that instead of changing the atom types by analogy to ones with the desired parameter already assigned, that instead one should assign bonded parameters by analogy. I was just wondering how this is better? I didn't suggest that. I said that any assignment by analogy can have negative outcomes. Bonds and angles, in theory, are a bit easier to deal with because the nonbonded interactions between their atoms are excluded. Torsions are very difficult because the torsional bonded terms have to be balanced against the charge and LJ parameters of atoms separated by 3 bonds, i.e. 1-4 interactions. Let me state very clearly that, for any missing parameters, anything short of a thorough parametrization and validation is (in my purist mind) unsound. As long as the atom type isnt too different, then why would the torsions not work out right? If the parameters are interrelated, what makes it better to add one term to an atom type rather than changing all the terms (to ones that are supposed to be together)? The key is being sufficiently similar, but even subtle differences between LJ parameters have very large consequences, especially for 1-4 interactions, so I find it hard to believe that one will recapitulate accurate interactions in this case. Of course, all assignments by analogy bear some penalty for nonequivalent groups. I balked at your initial post in the other thread because there was no need to mess with atom types. The system at hand there contained protein and lipid and could be completely described by existing atom types and bonded types, the OP there was just (and perhaps still is) constructing the force field incorrectly. I felt it need to be stated that the approach there would not necessarily be productive, and to make sure the archive was complete so that no one would come across a post in vacuum and assume that he or she can simply swap around atom types to make error messages go away. Your initial statement referred only to bonds and angles, which indeed would be insensitive to changes in LJ parameters on any of those atoms, but since the thread was in the context of dihedrals, I thought I should state my opinion there. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.edu jalemkul@outerbanks.** umaryland.edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usershttp://lists.gromacs.org/**mailman/listinfo/gmx-users htt**p://lists.gromacs.org/mailman/**listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchh**ttp://www.gromacs.org/Support/** Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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
Re: [gmx-users] changing atom types versus adding dihedrals to atom types
On 9/17/13 8:18 PM, Rafael I. Silverman y de la Vega wrote: Can you give some examples of how these verifications are different for different force fields? It doesnt seem like verifying takes that much time, but a theorist prof in my department told me not to worry as long as my system doesnt blow up... IMHO simply not blowing up tells you nothing. I can show you a dozen simulations that don't blow up that have terrible small molecule topologies that produce bad results. Parametrization methods and validation procedures are defined in the literature and one could easily fill a book chapter (or more) on such topics, so I will not go into it in an email. You may have to go back several years (or even decades) in the literature to get the full story. And what do you mean thourough parametrization? Most people hope for a simple, one-shot step they can take to parametrize a small molecule. There are numerous black box methods out there, some good and some bad. I advise people to be thorough in terms of what the force field requires and what their chemical knowledge tells them. For instance, for water interactions in CHARMM, HF/6-31G* works well for most compounds, unless sulfur is involved, in which case we need to do a more expensive MP2/6-31G* calculation. You can get an OK result for everything with HF, but it's not sufficiently accurate in all cases. I parametrized flavin mononucleotide using amber99sb-ildn, I used existing atomtypes in the force field, but I added partial atomic charges based on a decent DFT calculation in orca, and I had to add 2 distance restraints on the delta negatively charged phosphate oxygens to keep them from crashing into the delta positive hydrogen on the same phosphate. Is that thorough in your opinion? How does it compare with the results of running the molecule through antechamber? Usually GAFF gives a reasonable topology with minimal adjustment necessary. That's one of the benefits of Amber; there are very well-defined protocols and a robust general force field for the parametrization. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] changing atom types versus adding dihedrals to atom types
I see, when you say thorough parametrization and validation, what do you mean? How does one validate the system, calculate free energy in solution and compare it to tabulated data? On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote: Hi all, in another thread it was recommended that instead of changing the atom types by analogy to ones with the desired parameter already assigned, that instead one should assign bonded parameters by analogy. I was just wondering how this is better? I didn't suggest that. I said that any assignment by analogy can have negative outcomes. Bonds and angles, in theory, are a bit easier to deal with because the nonbonded interactions between their atoms are excluded. Torsions are very difficult because the torsional bonded terms have to be balanced against the charge and LJ parameters of atoms separated by 3 bonds, i.e. 1-4 interactions. Let me state very clearly that, for any missing parameters, anything short of a thorough parametrization and validation is (in my purist mind) unsound. As long as the atom type isnt too different, then why would the torsions not work out right? If the parameters are interrelated, what makes it better to add one term to an atom type rather than changing all the terms (to ones that are supposed to be together)? The key is being sufficiently similar, but even subtle differences between LJ parameters have very large consequences, especially for 1-4 interactions, so I find it hard to believe that one will recapitulate accurate interactions in this case. Of course, all assignments by analogy bear some penalty for nonequivalent groups. I balked at your initial post in the other thread because there was no need to mess with atom types. The system at hand there contained protein and lipid and could be completely described by existing atom types and bonded types, the OP there was just (and perhaps still is) constructing the force field incorrectly. I felt it need to be stated that the approach there would not necessarily be productive, and to make sure the archive was complete so that no one would come across a post in vacuum and assume that he or she can simply swap around atom types to make error messages go away. Your initial statement referred only to bonds and angles, which indeed would be insensitive to changes in LJ parameters on any of those atoms, but since the thread was in the context of dihedrals, I thought I should state my opinion there. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] changing atom types versus adding dihedrals to atom types
On 9/12/13 7:04 PM, Rafael I. Silverman y de la Vega wrote: I see, when you say thorough parametrization and validation, what do you mean? How does one validate the system, calculate free energy in solution and compare it to tabulated data? The target data depend on the force field for which parameters are being developed. Matching QM geometries, water interaction energies and distances, free energies of solvation, crystal structures, liquid properties, etc. are all useful depending on the underlying force field and how it was derived. For bonded parameters, matching QM energy scans and/or vibrational properties are common. -Justin On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote: Hi all, in another thread it was recommended that instead of changing the atom types by analogy to ones with the desired parameter already assigned, that instead one should assign bonded parameters by analogy. I was just wondering how this is better? I didn't suggest that. I said that any assignment by analogy can have negative outcomes. Bonds and angles, in theory, are a bit easier to deal with because the nonbonded interactions between their atoms are excluded. Torsions are very difficult because the torsional bonded terms have to be balanced against the charge and LJ parameters of atoms separated by 3 bonds, i.e. 1-4 interactions. Let me state very clearly that, for any missing parameters, anything short of a thorough parametrization and validation is (in my purist mind) unsound. As long as the atom type isnt too different, then why would the torsions not work out right? If the parameters are interrelated, what makes it better to add one term to an atom type rather than changing all the terms (to ones that are supposed to be together)? The key is being sufficiently similar, but even subtle differences between LJ parameters have very large consequences, especially for 1-4 interactions, so I find it hard to believe that one will recapitulate accurate interactions in this case. Of course, all assignments by analogy bear some penalty for nonequivalent groups. I balked at your initial post in the other thread because there was no need to mess with atom types. The system at hand there contained protein and lipid and could be completely described by existing atom types and bonded types, the OP there was just (and perhaps still is) constructing the force field incorrectly. I felt it need to be stated that the approach there would not necessarily be productive, and to make sure the archive was complete so that no one would come across a post in vacuum and assume that he or she can simply swap around atom types to make error messages go away. Your initial statement referred only to bonds and angles, which indeed would be insensitive to changes in LJ parameters on any of those atoms, but since the thread was in the context of dihedrals, I thought I should state my opinion there. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] changing atom types versus adding dihedrals to atom types
On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote: Hi all, in another thread it was recommended that instead of changing the atom types by analogy to ones with the desired parameter already assigned, that instead one should assign bonded parameters by analogy. I was just wondering how this is better? I didn't suggest that. I said that any assignment by analogy can have negative outcomes. Bonds and angles, in theory, are a bit easier to deal with because the nonbonded interactions between their atoms are excluded. Torsions are very difficult because the torsional bonded terms have to be balanced against the charge and LJ parameters of atoms separated by 3 bonds, i.e. 1-4 interactions. Let me state very clearly that, for any missing parameters, anything short of a thorough parametrization and validation is (in my purist mind) unsound. As long as the atom type isnt too different, then why would the torsions not work out right? If the parameters are interrelated, what makes it better to add one term to an atom type rather than changing all the terms (to ones that are supposed to be together)? The key is being sufficiently similar, but even subtle differences between LJ parameters have very large consequences, especially for 1-4 interactions, so I find it hard to believe that one will recapitulate accurate interactions in this case. Of course, all assignments by analogy bear some penalty for nonequivalent groups. I balked at your initial post in the other thread because there was no need to mess with atom types. The system at hand there contained protein and lipid and could be completely described by existing atom types and bonded types, the OP there was just (and perhaps still is) constructing the force field incorrectly. I felt it need to be stated that the approach there would not necessarily be productive, and to make sure the archive was complete so that no one would come across a post in vacuum and assume that he or she can simply swap around atom types to make error messages go away. Your initial statement referred only to bonds and angles, which indeed would be insensitive to changes in LJ parameters on any of those atoms, but since the thread was in the context of dihedrals, I thought I should state my opinion there. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
