I really don't think you can get adequate sampling for IDPs that have 40 residues, using full atomic MD.
On Wed, Jun 8, 2011 at 3:25 PM, Michael Daily <mdaily.w...@gmail.com> wrote: > Do you have some experimental data to compare to your IDP simulations, > like X-ray scattering or some such? I'd imagine that IDP simulations with > either forcefield would only be qualitatively accurate given that the > forcefields are calibrated, as you say, on rigid proteins and small > molecules. > > On 6/8/11 8:00 AM, Thomas Evangelidis wrote: > > Dear Prof van der Spoel and GROMACS users, > > I have read the article "Scrutinizing Molecular Mechanics Force Fields..." > where it is demonstrated that AMBER99sb yields protein conformations that > are in better agreement with residual dipolar coupling, J-coupling and NOE > data, compared with other force fields. However, both proteins used for this > benchmark study (ubiquitin and protein G) are rather rigid, so I was > wondering if there is a similar analysis for flexible proteins/peptides. I > want to simulate a few intrinsically disordered proteins/peptides of length > between 40 and 100 aa and would like to know what would be the best choice > of force field to use. Any experience or knowledge on this matter would be > greatly appreciated! > > thanks in advance, > Thomas > > > > On 27 May 2011 19:01, David van der Spoel <sp...@xray.bmc.uu.se> wrote: > >> On 2011-05-27 17.50, simon sham wrote: >> >>> Hi, >>> I have recently done two simulations on a protein at high temperature >>> near its melting temperature. At the beginning I used CHARMM forcefield, >>> and then OPLSAA to double check the results. There are some differences >>> in the structures between the forcefield used. I know different >>> forcefields can give different results. All parameters in the >>> simulations were the same except the forcefield. Is there anyway I can >>> tell which forcefield gives more reliable results? >>> >>> Thanks for the insights, >>> >>> Simon >>> >>> You might want to check >> >> 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) >> >> where we compare a number of FFs to NMR data. >> >> -- >> 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.se http://folding.bmc.uu.se >> >> -- >> 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 www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > > ====================================================================== > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tev...@bioacademy.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > > -- > Michael D. Daily, Ph.D. > Postdoctoral Fellow > Qiang Cui group > Department of Chemistry > University of Wisconsin-Madison > > > -- > 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 > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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