Hello, I've tried a couple ways of running the workshop tutorial with a different protein and amber03 force field. It works with a clean install of gromacs, but I am trying to integrate it into a grid computing project. https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
I tried several approaches to running this app but encountered a strange problem in both approaches to integrating. It always has trouble minimizing. This indicates to me, there is something strange with the environment that I created. If you have any hints for me that would be great. The two approaches I tried were: 1) putting all the dependent files in the same directory as the binary and executing it, this failed when I tested it stand alone and it created this same error 2) I tried writing a bash script to mimics the GMXRC.bash except it maps every directory relative to a temporary directory where everything runs. (e.g. GMXBIN=../slot/0/bin/) It seems to run fine through a workunit but then it does not minimize properly causing additional problems downstream Steepest Descents converged to machine precision in 54 steps, but did not reach the requested Fmax < 10. Potential Energy = -8.35030867755191e+214 Maximum force = 7.83437759695905e+221 on atom 25439 Norm of force = 5.13628303396235e+219 http://www.hydrogenathome.org/result.php?resultid=1341858 -- Jack http://www.facebook.com/home.php#/profile.php?id=832713248 http://hydrogenathome.org _______________________________________________ gmx-users mailing list [email protected] http://www.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
