Re: [gmx-users] Force fields, is there a review article?
On 2012-08-25 13:07, Luca Mollica wrote: I have read a variation on this advice many. many times here: "The ultimate choice of force field should be based on your reading and understanding of their derivation and known applications/limitations, all of which comes from the literature. Choose the one that you think is most sound :)" I am probably not the only person here who is attempting to learn and use molecular dynamics software for the first time. I am probably not the only person here who is trying to simulate a molecule for which there is NO published molecular dynamics study. Sure, it's a protein in water. Is that enough to tell me which force field(s) will give me a representative result, or not? maybe one of the best thing to do is to test the FF vs experimental data and check which one reproduces them better or provides more stability. a recent example, a bit oriented toward a particular field of research but interested in terms of methodology used is the following one by David Case: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997720/. this sentence explains you why:"The high resolution of the diffraction data (0.96Å) and the simplicity of the crystallization solution (nearly pure water) makes it possible to attribute any inconsistencies between the crystal structure and our simulations to artifacts of the models rather than inadequate representation of the crystal environment or uncertainty in the experiment.". it's not a problem of how it sounds, but if it "works" in sense of reproducing exprimental data, indeed. being a person that works in the world of NMR, I am always interested in FF that are tested against experimental data in my field, so this paper is interesting too: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/?tool=pmcentrez. like many papers written by Raphael Bruschweiler (like this: http://spin.magnet.fsu.edu/pubs/li_g28-g8_jctc2011.pdf). this one is relevant for AMBER FF lovers (like me) but also because it enters a bit in depth in the details of the delicate but necessary operation of improving a FF (a thing we experimentalists that use MD always have to trust but, I think, with a careful and critical eye kept on the problem): http://www.ncbi.nlm.nih.gov/pubmed/16981200. water is crytical too, a bit is written in the David Case paper I have cited but even more can be found in literature (I am not an expert in this topics). maybe someone else in the ML can be more helpful than me about this. We have done a couple of evaluations recently Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel & Carl Caleman: Structural stability of electrosprayed proteins: temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp. 8069-8078 (2009) http://dx.doi.org/10.1039/b903846a Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa, David van der Spoel: Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Compressibility, Expansion Coefficient and Dielectric Constant J. Chem. Theor. Comput. 8 pp. 61-74 (2012) http://pubs.acs.org/doi/abs/10.1021/ct200731v Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing Molecular Mechanics Force Fields on the Microsecond Timescale With NMR Data Biophys. J. 99 pp. 647-655 (2010) http://dx.doi.org/10.1016/j.bpj.2010.04.062 I search through abstracts in molecular dynamics at the library, but I never seem to find articles which are general enough. It would be very helpful if someone more knowledgeable in the field could point us newcomers at a review article, even a somewhat dated one, which surveys the use and utility of a few different force fields. It would be a good starting point. this one seems to be a thing of the kind you are looking for, but I don't know it even though it seems interesting (just found googling the title of other papers I have just listed): http://maxwell.uncc.edu/abaumket/phys6203_files/Reading/force-fields.pdf Regards. L -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Force fields, is there a review article?
I have read a variation on this advice many. many times here: "The ultimate choice of force field should be based on your reading and understanding of their derivation and known applications/limitations, all of which comes from the literature. Choose the one that you think is most sound :)" I am probably not the only person here who is attempting to learn and use molecular dynamics software for the first time. I am probably not the only person here who is trying to simulate a molecule for which there is NO published molecular dynamics study. Sure, it's a protein in water. Is that enough to tell me which force field(s) will give me a representative result, or not? maybe one of the best thing to do is to test the FF vs experimental data and check which one reproduces them better or provides more stability. a recent example, a bit oriented toward a particular field of research but interested in terms of methodology used is the following one by David Case: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997720/. this sentence explains you why:"The high resolution of the diffraction data (0.96Å) and the simplicity of the crystallization solution (nearly pure water) makes it possible to attribute any inconsistencies between the crystal structure and our simulations to artifacts of the models rather than inadequate representation of the crystal environment or uncertainty in the experiment.". it's not a problem of how it sounds, but if it "works" in sense of reproducing exprimental data, indeed. being a person that works in the world of NMR, I am always interested in FF that are tested against experimental data in my field, so this paper is interesting too: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2905107/?tool=pmcentrez. like many papers written by Raphael Bruschweiler (like this: http://spin.magnet.fsu.edu/pubs/li_g28-g8_jctc2011.pdf). this one is relevant for AMBER FF lovers (like me) but also because it enters a bit in depth in the details of the delicate but necessary operation of improving a FF (a thing we experimentalists that use MD always have to trust but, I think, with a careful and critical eye kept on the problem): http://www.ncbi.nlm.nih.gov/pubmed/16981200. water is crytical too, a bit is written in the David Case paper I have cited but even more can be found in literature (I am not an expert in this topics). maybe someone else in the ML can be more helpful than me about this. I search through abstracts in molecular dynamics at the library, but I never seem to find articles which are general enough. It would be very helpful if someone more knowledgeable in the field could point us newcomers at a review article, even a somewhat dated one, which surveys the use and utility of a few different force fields. It would be a good starting point. this one seems to be a thing of the kind you are looking for, but I don't know it even though it seems interesting (just found googling the title of other papers I have just listed): http://maxwell.uncc.edu/abaumket/phys6203_files/Reading/force-fields.pdf Regards. L -- Luca Mollica Protein Dynamics and Flexibility by NMR Institut de Biologie Structurale "Jean-Pierre Ebel" UMR 5075 CNRS/CEA/UJF 41 rue Jules Horowitz 38027 Grenoble Cedex 01 E-mail: luca.moll...@ibs.fr lucamollica...@gmail.com Skype:lucamollica Linkedin: http://fr.linkedin.com/in/lucamollica Tel: +33.(0)438783889 Fax: +33.(0)438785494 We need not destroy the past. It is gone. (J.Cage) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] Force fields, is there a review article?
I have read a variation on this advice many. many times here: "The ultimate choice of force field should be based on your reading and understanding of their derivation and known applications/limitations, all of which comes from the literature. Choose the one that you think is most sound :)" I am probably not the only person here who is attempting to learn and use molecular dynamics software for the first time. I am probably not the only person here who is trying to simulate a molecule for which there is NO published molecular dynamics study. Sure, it's a protein in water. Is that enough to tell me which force field(s) will give me a representative result, or not? I search through abstracts in molecular dynamics at the library, but I never seem to find articles which are general enough. It would be very helpful if someone more knowledgeable in the field could point us newcomers at a review article, even a somewhat dated one, which surveys the use and utility of a few different force fields. It would be a good starting point. Thanks! -- View this message in context: http://gromacs.5086.n6.nabble.com/Force-fields-is-there-a-review-article-tp5000519.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
