Re: [gmx-users] Limitations of simulations?
On 2013-07-24 01:57, Jonathan Saboury wrote: I just finished this tutorial and found it very informative: http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf However, This was based on a complex from a pdb. I was wondering if it was possible to just simulate the protein without complex and put the ligand as a solute and actually have it complex with the protein. Obviously, if it could do this it would take a much longer time than just simulating a complex, but if given enough time, could it complex? Yes, there are some examples. A paper was published by Shaw and co-worker in J. Amer. Chem. Soc. a year or two ago. I have no formal experience with simulations and currently have no one around me with enough knowledge on these topic to mentor me, so any help is very much appreciated! Thank you! :) -- 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 * 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] Limitations of simulations?
On 7/24/13 6:44 AM, David van der Spoel wrote: On 2013-07-24 01:57, Jonathan Saboury wrote: I just finished this tutorial and found it very informative: http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf However, This was based on a complex from a pdb. I was wondering if it was possible to just simulate the protein without complex and put the ligand as a solute and actually have it complex with the protein. Obviously, if it could do this it would take a much longer time than just simulating a complex, but if given enough time, could it complex? Yes, there are some examples. A paper was published by Shaw and co-worker in J. Amer. Chem. Soc. a year or two ago. I have no formal experience with simulations and currently have no one around me with enough knowledge on these topic to mentor me, so any help is very much appreciated! For the rest of us mere mortals who don't have access to specialized hardware that allows for 10- or 20-microsecond simulations, the brute force approach is rather futile. Techniques like steered MD and Hamiltonian replica exchange MD are probably more feasible. Unbiased simulations of sufficient length, using standard supercomputing hardware, would probably take years. -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] Limitations of simulations?
On 7/24/13 9:16 PM, Jonathan Saboury wrote: For the rest of us mere mortals who don't have access to specialized hardware that allows for 10- or 20-microsecond simulations, the brute force approach is rather futile. Techniques like steered MD and Hamiltonian replica exchange MD are probably more feasible. Unbiased simulations of sufficient length, using standard supercomputing hardware, would probably take years. -Justin Do you think implicit water with 10-20 ligands would be able to do it? I see that the gpu accelerated implicit gets about 100-150 ns/day so a 10-20 day simulation would yield that time frame, no? Thanks :) In an implicit, non-periodic system, it is more likely that the ligand will float away from the protein. I've tried it and that's all that ever happens. Moreover, the current Gromacs version does not support implicit solvent on GPU and the previous version that did had very limited functionality. -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] Limitations of simulations?
I would like to stop to receive this e-mail, how can i procide?Thanks Fábio Filippi MatioliGraduando em Física MédicaUNESP-BotucatuTel (19) 9291.6738 Date: Tue, 23 Jul 2013 22:57:29 -0700 From: jsab...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Limitations of simulations? I just finished this tutorial and found it very informative: http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf However, This was based on a complex from a pdb. I was wondering if it was possible to just simulate the protein without complex and put the ligand as a solute and actually have it complex with the protein. Obviously, if it could do this it would take a much longer time than just simulating a complex, but if given enough time, could it complex? I have no formal experience with simulations and currently have no one around me with enough knowledge on these topic to mentor me, so any help is very much appreciated! Thank you! :) -- 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 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
