Re: [gmx-users] How to increase the tolerance for conjugate gradient minimization
Hi Arthur, Two answers: It's a pretty fundamental result on numerical analysis that you can only achieve a tolerance that is sqrt(EPS), where EPS is your floating-point accuracy. If you need better tolerance you might have to try double precision. Be careful to use e.g. switched interactions and a cutoff buffer, and you might want to emply L-BFGS minimization in the endgame. However: this assumes you really need extremely low tolerance - the only normal application where that is the case is normal modes. Cheers, Erik On Jun 4, 2010, at 7:54 PM, Arthur Roberts wrote: 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. Much appreciated, Art Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences 9500 Gilman Drive #0703 La Jolla, CA 92093-0703 email: aroberts99...@yahoo.com cell: 206-850-7468 skype=aroberts92122 -- gmx-users mailing listgmx-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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Erik Lindahl lind...@cbr.su.se Professor, Computational Structural Biology Center for Biomembrane Research Swedish e-Science Research Center Department of Biochemistry Biophysics, Stockholm University Tel: +468164675 Cell: +46703844534 -- gmx-users mailing listgmx-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
Re: [gmx-users] How to increase the tolerance for conjugate gradient minimization
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 listgmx-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 listgmx-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
Re: [gmx-users] How to increase the tolerance for conjugate gradient minimization
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. +41-44-639 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 listgmx-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 listgmx-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
Re: [gmx-users] How to increase the tolerance for conjugate gradient minimization
- 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 listgmx-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
