I am not quite in the business of folding/unfolding protein. On Sun, Oct 12, 2014 at 4:07 PM, Johnny Lu <johnny.lu...@gmail.com> wrote:
> Thank you for pointing me to that paper. I took a quick look of it > yesterday. > Would the results in the paper stay the same, if the side chain rotations > of a protein is investigated? > > On Sun, Oct 12, 2014 at 3:30 PM, Michael Shirts <mrshi...@gmail.com> > wrote: > >> > 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? 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