Hi Arthur, The most useful option from my experience is to run Gromacs in double precision. You also can try to make emstep smaller (after an initial minimisation of the crude structure) and use l-bfgs.
Good luck, Ran -- ------------------------------------------------------ Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355559 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman ------------------------------------------------------ Arthur Roberts wrote: > I agree the code is fine. Is there a parameter that I need to change > to increase the tolerance? I have issues energy minimizing a small > molecule in the presence of a macromolecule. One work around is to > increase the energy of the small molecule, so that the macromolecule > no longer dominates the energetics. I would appreciate your input. > > Art > > On Jun 4, 2010, at 5:45 PM, Mark Abraham wrote: > >> >> >> ----- Original Message ----- >> From: Arthur Roberts <aroberts99...@yahoo.com> >> Date: Saturday, June 5, 2010 4:57 >> Subject: [gmx-users] How to increase the tolerance for conjugate >> gradient minimization >> To: gmx users <gmx-users@gromacs.org> >> >> > Hi, all, >> > >> > Is there a way to increase the tolerance for Conjugate Gradient >> > energy minimization? >> > >> > It seems that I can only get a Tolerance (Fmax) = 1e-4 >> > >> > emtol doesn't seem to do the trick. I tried several values. >> >> The code's fine in 4.0.7. Does your .mdp value match that reported in >> the .log file? Ditto in gmxcheck on the .tpr? >> >> Mark -- >> 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/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/mailing_lists/users.php > > Art Roberts > 7254 Shoreline Dr. #130 > San Diego, CA 92122 > cell: 206-850-7468 > email: aroberts99...@yahoo.com > skype=aroberts92122 -- 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/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/mailing_lists/users.php
