Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time.
Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: > Won't this same stochastic nature of MD provide for different, independent > trajectories even if restarted from a previous, equilibrated frame even > without resetting velocities, i.e., as a continuation run using the > velocities recorded in the gro file of the selected snapshot? > > Felipe > > On 11/22/2012 12:55 AM, Mark Abraham wrote: >> Generating velocities from a new random seed is normally regarded as good >> enough. By the time you equilibrate, the chaotic nature of MD starts to >> work for you. >> >> Mark >> On Nov 21, 2012 1:04 PM, "Felipe Pineda, PhD" <luis.pinedadecas...@lnu.se> >> wrote: >> >>> So how would you repeat the (let be it converged) simulation from >>> different starting conditions in order to add that valuable statistics you >>> mention? >>> >>> I think this was Albert's question >>> >>> Felipe >>> >>> On 11/21/2012 12:41 PM, Mark Abraham wrote: >>> >>>> If a simulation ensemble doesn't converge reliably over a given time >>>> scale, >>>> then it's not converged over that time scale. Repeating it from different >>>> starting conditions still adds valuable statistics, but can't be a >>>> replicate. Independent replicated observations of the same phenomenon >>>> allow >>>> you to assess how likely it is that your set of observations reflect the >>>> underlying phenomenon. The problem in sampling-dependent MD is usually in >>>> making an observation (equating a converged simulation with an >>>> observation). >>>> >>>> Mark >>>> >>>> On Wed, Nov 21, 2012 at 8:12 AM, Albert <mailmd2...@gmail.com> wrote: >>>> >>>> hello: >>>>> I am quite confused on how to repeat our MD in Gromacs. If we started >>>>> from the same equilibrated .gro file with "gen_vel = no" in >>>>> md.mdp, >>>>> we may get "exactly" the same results which cannot be treated as >>>>> reasonable >>>>> repeated running. However, if we use "gen_vel=yes" for each round of >>>>> running, sometimes our simulation may not converged at our simulated time >>>>> scale and we may get two results with large differences. >>>>> >>>>> So I am just wondering how to perform repeated MD in Gromacs in a >>>>> correct way so that our results can be acceptably repeated? >>>>> >>>>> thank you very much. >>>>> Albert >>>>> -- > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > 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 ----------------------------------------------- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 6688 fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
