Hi, You can try the non-gromacs tool Concoord: http://www.mpibpc.mpg.de/groups/de_groot/concoord/ http://151.100.52.62/pdf/046_amadei_proteins_1997.pdf
It was used e.g. in the CC/PBSA algorithm http://ccpbsa.biologie.uni-erlangen.de/ccpbsa/ http://www.nature.com/nmeth/journal/v6/n1/full/nmeth0109-3.html ---------------------------------------------------------------------- Message: 1 Date: Mon, 10 Oct 2011 10:04:30 -0500 From: "Liu, Liang" <[email protected]> Subject: [gmx-users] How to obtain structures with large RMSD? To: Discussion list for GROMACS users <[email protected]> Message-ID: <CABxJRoJ5MgcYx02c5CqjtbU8HhEdh1=cyu1eggzzqeot0_+...@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi, all, I am trying to use Gromacs to obtain structural ensembles around native structures (PDB structures). However the simulated structures are always very close to the initial one, with RMSD < 0.2. I am wondering how to obtain large-RMSD structures? Thanks. -- Best, Liang Liu -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
