Re: [gmx-users] More suitable force field and water model
There is no best combination. The parameters for water for your solute must be derived using physically equivalent procedures. That's all. Dr. Vitaly V. Chaban On Thu, Jun 19, 2014 at 11:59 AM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose. As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. I think it is also related to properties of our system components (charge, etc.). for example for sugars or lipids. Is there any article which has compared these in details? Please let me know. any suggestion is appreciated in advance Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] More suitable force field and water model
On 6/20/14, 3:36 AM, Mohsen Ramezanpour wrote: Hi Mark, You are right. :-) regarding quantities I mentioned (e.g, free energies and active site structure properties): How if we simulate our system twice? once using Gromos 53a6 and its parametrized water model (SPC, I guess) to estimate free energies and the second time using another force field which will not result in instability! In this way we can ensure our results are more precise. Of course it will cost more time. Please let me know your point of view about it. Well, if you calculate a binding free energy to a structure that may not be sufficiently stable or may sample nonphysical structures, then the binding free energy will probably be wrong. The 54a7 parameter set improved helical stability and is based on the same principles as 53a6, so I would say just move on from 53a6. -Justin On Thu, Jun 19, 2014 at 8:59 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, It would be miraculous if there was a good solution for all observables. A rigid, symmetric 3-point water molecule without VDW parameters on the the hydrogen atoms has 2 spatial, 2 charge, and 2 VDW parameters. That's not much freedom, and most of the 6-parameter space is obviously wrong, too. All you can do is pick a model that does something right (e.g. was the one used to parameterize the force field), accept that your model physics is a model, and remain alert for known and new problems. Even the quantum chemists argue about how to model small clusters of water! ;-) Mark On Thu, Jun 19, 2014 at 3:55 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Justin, On Thu, Jun 19, 2014 at 3:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/19/14, 5:59 AM, Mohsen Ramezanpour wrote: Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose. This is actually very straightforward. Every force field was parametrized using a certain water model. That's the one you use unless there is clear evidence that a different model works better for some reason. There are very few deviations from the original parametrizations of which I am aware, and most improvements are only small. As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Without context, there's not much value to that statement. On their own, some water models reproduce certain bulk properties better than others, but no water model is perfect. If you were to combine TIP4P with Gromos or something, I'd say that's probably unsound, even if TIP4P is better in terms of whatever you've chosen to look at. Yes, Please have a look at the abstract ( http://www.ncbi.nlm.nih.gov/pubmed/16178604) and also the conclusion of ( http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482 ) What do you mean exactly by something? do you mean TIP4P does not behave good enough in combination with other force fields too?! Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. That's not necessarily true; I've seen demonstrations of other combinations yielding very good hydration free energies. You are right, but some of them give more precise results and work for most cases! The conclusion of ( http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482 ) In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. If you're using Gromos96 53a6, it is known to produce helical instability. So the hydration free energies may be good, but the structure of the protein may suffer from artifacts. Yes, I want to use this ff because of our main quantities of interest. But we also are interested in other quantities (for example our active site structure which is composed of helices, its flexibility, etc). the main problem I mentioned was: How can we rely on other quantities from our simulation while we have chosen some special combinations? No body has
[gmx-users] More suitable force field and water model
Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose. As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. I think it is also related to properties of our system components (charge, etc.). for example for sugars or lipids. Is there any article which has compared these in details? Please let me know. any suggestion is appreciated in advance Best Regards -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] More suitable force field and water model
On 6/19/14, 5:59 AM, Mohsen Ramezanpour wrote: Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose. This is actually very straightforward. Every force field was parametrized using a certain water model. That's the one you use unless there is clear evidence that a different model works better for some reason. There are very few deviations from the original parametrizations of which I am aware, and most improvements are only small. As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Without context, there's not much value to that statement. On their own, some water models reproduce certain bulk properties better than others, but no water model is perfect. If you were to combine TIP4P with Gromos or something, I'd say that's probably unsound, even if TIP4P is better in terms of whatever you've chosen to look at. Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. That's not necessarily true; I've seen demonstrations of other combinations yielding very good hydration free energies. In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. If you're using Gromos96 53a6, it is known to produce helical instability. So the hydration free energies may be good, but the structure of the protein may suffer from artifacts. I think it is also related to properties of our system components (charge, etc.). for example for sugars or lipids. Is there any article which has compared these in details? Please let me know. dx.doi.org/10.1021/jp0641029 -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] More suitable force field and water model
Dear Justin, On Thu, Jun 19, 2014 at 3:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/19/14, 5:59 AM, Mohsen Ramezanpour wrote: Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose. This is actually very straightforward. Every force field was parametrized using a certain water model. That's the one you use unless there is clear evidence that a different model works better for some reason. There are very few deviations from the original parametrizations of which I am aware, and most improvements are only small. As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Without context, there's not much value to that statement. On their own, some water models reproduce certain bulk properties better than others, but no water model is perfect. If you were to combine TIP4P with Gromos or something, I'd say that's probably unsound, even if TIP4P is better in terms of whatever you've chosen to look at. Yes, Please have a look at the abstract ( http://www.ncbi.nlm.nih.gov/pubmed/16178604) and also the conclusion of ( http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482) What do you mean exactly by something? do you mean TIP4P does not behave good enough in combination with other force fields too?! Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. That's not necessarily true; I've seen demonstrations of other combinations yielding very good hydration free energies. You are right, but some of them give more precise results and work for most cases! The conclusion of ( http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482) In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. If you're using Gromos96 53a6, it is known to produce helical instability. So the hydration free energies may be good, but the structure of the protein may suffer from artifacts. Yes, I want to use this ff because of our main quantities of interest. But we also are interested in other quantities (for example our active site structure which is composed of helices, its flexibility, etc). the main problem I mentioned was: How can we rely on other quantities from our simulation while we have chosen some special combinations? No body has investigated all quantities of simulation for all ff and water models combinations, what can be the solution? I think it is also related to properties of our system components (charge, etc.). for example for sugars or lipids. Is there any article which has compared these in details? Please let me know. dx.doi.org/10.1021/jp0641029 Some of my comments was from the same article! please have a look at the abstract and conclusion Thanks in advance -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] More suitable force field and water model
Hi, It would be miraculous if there was a good solution for all observables. A rigid, symmetric 3-point water molecule without VDW parameters on the the hydrogen atoms has 2 spatial, 2 charge, and 2 VDW parameters. That's not much freedom, and most of the 6-parameter space is obviously wrong, too. All you can do is pick a model that does something right (e.g. was the one used to parameterize the force field), accept that your model physics is a model, and remain alert for known and new problems. Even the quantum chemists argue about how to model small clusters of water! ;-) Mark On Thu, Jun 19, 2014 at 3:55 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Justin, On Thu, Jun 19, 2014 at 3:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/19/14, 5:59 AM, Mohsen Ramezanpour wrote: Dear Gromacs Users, I have read some articles about the more appropriate combination of force field and water model for different simulations of interest. It is confusing and too difficult to decide which combination is the best one. Besides according to articles I read, I am in doubt now and not sure which combination should I choose. This is actually very straightforward. Every force field was parametrized using a certain water model. That's the one you use unless there is clear evidence that a different model works better for some reason. There are very few deviations from the original parametrizations of which I am aware, and most improvements are only small. As I understood, the SPC and TIP4P are recommended for biomolecular simulations and some authors have also recommended SPC. Without context, there's not much value to that statement. On their own, some water models reproduce certain bulk properties better than others, but no water model is perfect. If you were to combine TIP4P with Gromos or something, I'd say that's probably unsound, even if TIP4P is better in terms of whatever you've chosen to look at. Yes, Please have a look at the abstract ( http://www.ncbi.nlm.nih.gov/pubmed/16178604) and also the conclusion of ( http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482) What do you mean exactly by something? do you mean TIP4P does not behave good enough in combination with other force fields too?! Although SPC/E seems the best one in non-polarizable models for bulk properties of water but for different quantities of interest such as hydration free energy, hydration enthalpy, entropy, heat capacities etc. some special combinations will be more appropriate. I found that although using a FF+water model will result in a precise enough quantity but we can not rely on some other quantities of our simulation! By this I mean, If we are interested in hydration free energy, the best option seems to be Gromos 53a6 and SPC or SPC/E model. But if we are interested in other quantities as well, other combinations will be preferred. That's not necessarily true; I've seen demonstrations of other combinations yielding very good hydration free energies. You are right, but some of them give more precise results and work for most cases! The conclusion of ( http://scitation.aip.org/content/aip/journal/jcp/108/24/10.1063/1.476482) In fact I am interested in Protein-ligand binding free energy and also its Enthalpy and Entropy contributions as well. I guess in this case it is better to choose Gromos+SPC or SPC/E. But I am not sure. If you're using Gromos96 53a6, it is known to produce helical instability. So the hydration free energies may be good, but the structure of the protein may suffer from artifacts. Yes, I want to use this ff because of our main quantities of interest. But we also are interested in other quantities (for example our active site structure which is composed of helices, its flexibility, etc). the main problem I mentioned was: How can we rely on other quantities from our simulation while we have chosen some special combinations? No body has investigated all quantities of simulation for all ff and water models combinations, what can be the solution? I think it is also related to properties of our system components (charge, etc.). for example for sugars or lipids. Is there any article which has compared these in details? Please let me know. dx.doi.org/10.1021/jp0641029 Some of my comments was from the same article! please have a look at the abstract and conclusion Thanks in advance -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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
