Hello there, Concerning to the issue raised by Sana and "gmx cluster", what would be the potential known useful geometric criterion of amino acids in each of below systems:
1) A single amino acid in aqueous solution? 2) A single amino acid adsorbed on a solid surface in aqueous solution? Thanks. Regards, Alex On Thu, Jun 9, 2016 at 1:31 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/8/16 8:37 PM, Sana Saeed wrote: > >> hello gromacs users and experts, >> i have performed 10ns complex simulation of Protein and ligand-complex, >> now i need the best conformation for further analysis (alchemical analysis: >> binding free energy simulations). i want to choose best initial structure >> for further study. how would i know which frame has lowest energy? i >> studied gmx energy tool but couldn't find way. >> > > Cluster the trajectory based on some known useful geometric criterion. > The lowest energy state should be the most populated one. Note that > energies that come out of simulations are not free energies (at least, not > without significant post-processing and analysis) so you can't use e.g. > quantities from gmx energy to get an answer. 10 ns isn't likely long > enough to really get anything definitive, though. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > 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.
