oh, i still mix up things. the numerical error might act as dissipation. On Sun, Oct 12, 2014 at 3:01 PM, Johnny Lu <johnny.lu...@gmail.com> wrote:
> Sorry that I misunderstood your post. > > Can compensating energy lost caused by numerical error with thermostat > cause error in the probability distribution of thermodynamic variables and > distribution of conformations? > > Below is just a guess. I don't understand the fluctuation dissipation > theorem enough at this point. > > I would guess so.. unless the fluctuation of the velocity of the atom > doesn't follow maxwell-Boltzmann distribution (I guess that can happen in a > crystal made of harmonic oscillator of a single frequency, or if some part > of the protein has low degree of freedom. This is a flaw found in > nose-hover thermostats.) > > Otherwise, some thermostats already try to provide the correct > fluctuation, so that the distribution of thermodynamic variables is correct > (as in fluctuation-dissipation theorem). If we use thermostats, the > thermostats will correct the energy drop/raise caused by numerical error > (which acts as a fluctuating source/sink that may not even follow the > normal distribution), without causing additional artifacts. > > Regardless, thermostats causes artifacts, especially in dynamics and rates. > > On Sun, Oct 12, 2014 at 2:07 PM, Michael Shirts <mrshi...@gmail.com> > wrote: > >> > 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. >> > > -- 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.
