I believe that it's all described with reasonable detail in the manual. Erik
31 mar 2012 kl. 18.42 skrev Yun Shi: > Hi all, > > I am just wondering about how GROMACS works when coupling temperature and > pressure. > > Assuming the simplest coupling method, like Berendsen, does GROMACS just > scale down/ up kinetic energy (KE) for each particle in the system, such as > KE1/KE2 = T1/T2 ? Similarly for pressure, KE1/KE2 = P1/P2? So GROMACS scales > the square root of velocities for every particle after each time step? > > > ----------------------------------------------------------------- > BTW, the number of degrees of freedom = 3N - Nc - Ncom according to the > manual. For conventional MD, is Nc equal to the total number of constrained > bonds (like all bonds in gromos ff, and all bonds involving hydrogens in > amber99sb ff)? > > Thanks for any explanation. > > Yun > -- > 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html
-- 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
