Dear Justin and gmxers Thank you so much for your helpful hints, but I am wondering how to check if I have obtained "proper distributions for the desired ensemble", as suggested in your email? My thoughts are: 1. As for NVT ensemble, I need to check if the velocity (or speed) of molecules in my simulation follows a Maxwell-boltzmann distribution, and the velocity is for the center of mass of these molecules, not for individual atoms, right? 2. Can I also check the distribution of T in my simulation (I output T every 100 steps or so, and make a statistics)? It is said in NVT ensemble, T follows a gaussian distribution, according to central limit theorem, and the square of its variance is 2T*T/(3N). Is that correct? 3. As for NPT ensemble, how to check if I have get a correction distribution from pressure coupling? Can I also check the P or V distribution? If so, what is the correct distribution I should get? I find some clues at "Understanding Modern Molecular Dynamics J. Phys. Chem. B 2000, 104, 159-178", but this paper just discuss some simple systems in T,P coupling section, and I still do not know the correct distribution I should get for my own simulations (e.g. protein in a box of water, NPT). 4.Are there any other quantities I need to check to make sure I have sampled a correct ensemble? I think to check the distribution of v, T, P V should be enough for this purpose, lthough to check more quantities is a plus, right? Any suggestions or comments are very welcome. Thank you. yours xiaodong Research School of Chemistry ANU
On Tue, Jun 21, 2011 at 11:21 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > xiaodong huang wrote: > >> Dear gromacs-ers >> >> I am using stochastic dynamics integrator (integrator = sd), so most of >> the time, I only need to adjust following parameters for temperature and >> pressure coupling: tau_t pcoupl tau_p (ref_t is room temperature and ref_p >> is 1 atm, compressibility can be taken from experimental numbers). >> >> >> In the manual, a tau_t between 1 and 2ps is recommended for the sake of >> simulation stability, but I see someone use a tau_t of 0.1ps with the same >> integrator (integration was performed with Langevin dynamics,49 with a >> reference temperature of 300 K and a weak frictional constant of 10 ps-1,) >> when simulating water solvent. I also see someone use a tau_t of 0.2ps with >> the same integrator (To obtain a isothermal–isobaric ensemble at 293 K, a >> leap-frog stochastic dynamics integrator16 was used to integrate the >> equations of motion. The inverse friction constant was set to 0.2 ps.) when >> simulating some organic solvent. I check the references mentioned in these >> gromacs papers so I am pretty sure they are using the same integrator. So I >> am a bit confusing here, what tau_t should I use, the number between 1 and >> 2ps as recommended by the manual, or the numbers below 1ps, as reported in >> these papers? Does this parameter depend on what solvent (water, >> cyclohexane) I use? Can I just use any number between 0.1ps and 2ps and >> check if my simulations look fine or there is some ‘best’ number for a >> particular solvent? >> >> > This was discussed recently: > > http://lists.gromacs.org/**pipermail/gmx-users/2011-June/**061992.html<http://lists.gromacs.org/pipermail/gmx-users/2011-June/061992.html> > > > >> When I use berendsen or Parrinello-Rahman, the same questions apply: Is >> there some ‘best’ number for a particular solvent, or I can just use any >> number between 0.5ps and 5ps and check if my simulations run well? >> >> >> When I read papers, I find many different pressure coupling constant >> (tau_p) ranging from 0.5ps to 1ps (water), 1ps to 5ps (organic solvent) with >> weak coupling scheme in gromacs. I am wondering why they use bigger number >> for organic solvent? If I use Parrinello-Rahman (it is said to be better >> than berendsen in the manual), do I need to change tau_p, or I can just use >> the same tau_p as berendsen? >> >> > Time constants are a bit empirical. The Berendsen algorithm is more > forgiving; it relaxes very quickly and thus low values of tau_t/tau_p are > stable. For methods that allow for wider oscillations (N-H for temperature, > P-R for pressure), small tau_t/tau_p values are unstable due to the nature > of these algorithms. The most important information is whether or not you > obtain proper distributions for the desired ensemble. Any algorithm can be > made to behave artificially rigorously or artificially relaxed. > > -Justin > > > Thank you so much for your kind help, any suggestions or clues are very >> welcome. >> >> Yours >> >> xiaodong huang >> Research School of Chemistry >> ANU >> >> > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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