Hi Tsjerk, I ran my job on the same machine and made exactly the same inputstructure and inputfile. What does chaos mean in your opinion? A computer should do exactly the same every time you start with the same starting conditions on the same machine.
I have to couple my ligand seperately and not as part of my protein, so I can't couple just two groups named Protein and Non-Protein. Bests, Emanuel >>> Tsjerk Wassenaar 02/17/10 9:40 AM >>> Hi Emanuel, Anything small can cause trajectories to diverge, it's chaos. The machine on which is run can make the difference. This is also covered in the list archives. > ;Temperature coupling > tcoupl = nose-hoover > tc-grps = protein NA+ CFP SOL > tau_t = 0.1 0.1 0.1 0.1 > ref_t = 300 300 300 300 This is bad practice. Where did you get that from? Not from any _good_ tutorial, surely. Check http://www.gromacs.org/Documentation/Terminology/Thermostats to learn more. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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 -- 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
