On Thu, 09 Jun 2011 17:30:10 +0200 kalav...@gmx.net wrote: > Dear Gromacs-users, > > I compiled a single and a double precision version of gromacs 4.5.4 > (MPI enabled). The differences between single and double precision > runs have been discussed in older threads (2005/2008) in this mailing > list before. At least, I did not understand completely, which parts > or calculations in an simulation are affected by my single/double > precision choice. Some threads identified the equilibration step to > be the most susceptible for differences. Is this true ?
You might need to use double precision in minimization if your initial structure is pathological (very large forces). > With each version (single and double precision), I calculated the > same simulation (same seeds). Which observables/energies/tests should > I observe or conduct to find and evaluate the differences ? Since you're in any case modeling a chaotic system, single and double precision calculations might lead to completely different trajectories. What you would need to do is sample over many runs to get the ensemble right. You probably should observe just the observables that you are interested in. However, if you are using thermostats (or barostats), using double precision is mostly just a waste of resources, since the thermostat will just waste the extra precision. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.leht...@helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.leht...@helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
