> 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.
Thermostats correct SOME of the artifacts. It is not always clear which ones. > Regardless, thermostats causes artifacts, especially in dynamics and rates. In SOME cases it may be negligible. In others, not. It is very hard to say. See our paper linked before http://pubs.acs.org/doi/abs/10.1021/ct400109a "Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations" which covers most short-time scale effects. Whether the thermostats that do not affect short time scale properties to any noticable degree still affect long-time scale properties through some sort of error accumulation is not known, nor which properties they might affect. On Sun, Oct 12, 2014 at 3:07 PM, Johnny Lu <johnny.lu...@gmail.com> wrote: > 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. > -- 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.
