Hi Peng, AFAIK GMX only uses fftw for PME.
If you have no reason to prefer flexible bonds you can use LINCS or SHAKE to constrain the bond lengths and run with a timestep of 2fs at room temperature. You may want to try LAMMPS and GMX with SHAKE and a timestep of 2fs and see if the results are similar before recompiling GMX. If I understood you correctly you didn't constrain the bonds. Ran Peng Yi wrote: > > Hi, Ran, > > Do you mean the simulation I used here for testing purpose? That is > not long, maybe a few hours. But my research will require simulations > for days. If I will not use PME, do I still need a fftw? > > -Peng > > On Wed, 4 Nov 2009, Ran Friedman wrote: > >> Hi Peng, >> >> It would be slower - never made any benchmarks on how much slower. But >> you don't run a very long simulation, do you? >> Installing it isn't a problem. If you use PME you also need fftw in >> double precision though. >> >> Ran >> >> Peng Yi wrote: >>> >>> Hi, Ran, >>> >>> No, I haven't. I still have to find out how to install in double >>> precision. Would double precision be slower than single? If so, >>> how much? Or just double the memory used? Thanks, >>> >>> -Peng >> >> _______________________________________________ >> 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 _______________________________________________ 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
