> The point was that if the energy leaves the system, then the system is never in equilibrium. Not vice versa, please.
This is incorrect logic. f there are errors in the integrator, then F=gradient of the potential is not true. If that is not true, energy is not conserved, and energy can leave or enter the system. On Sun, Oct 12, 2014 at 1:58 PM, Dr. Vitaly Chaban <vvcha...@gmail.com> wrote: > The point was that if the energy leaves the system, then the system is > never in equilibrium. Not vice versa, please. > > > > Dr. Vitaly V. Chaban > > Виталий Витальевич ЧАБАН > > > On Sun, Oct 12, 2014 at 7:20 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > > Why non-equilibrium can cause lost of total energy in NVE simulation? > > (baring the case that the non-equilibrium causes very large values that > > causes over flow / getting out of the stable range of algorithms of > > gromacs). > > > > A closed system should have constant energy, regardless of whether it is > at > > equilibrium. > > > > I guess people use the word "converge" instead of equilibrium in > molecular > > dynamics simulation of protein, possibly because the simulation may never > > reach equilibrium with current computing power. > > http://pubs.rsc.org/en/content/articlepdf/2012/cp/c2cp23961b > > > > I may try older version of gromacs and/or not using constraint, after > > checking the bug list and performance. I had never thought about that > route. > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
