Hi, many thanks. I am doing some simulation correlated with the growth, in experiments, there are two kinds of growth, one is driven by kinetics and other is by thermodynamics. So I just wonder to know by using MD simulations, the results I obtained is driven by kinetics or thermodynamics.
Silly question. XJ 2011/9/26 Mark Abraham <mark.abra...@anu.edu.au> > On 26/09/2011 5:31 PM, xiaojing gong wrote: > > Hi, many thanks for your answer. > > >> Any dynamical simulation has a lowest-energy structure... whether this > means anything is another question. > > I am just wondering whether the structures you find with MD determined > mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics > (i.e. the structures > with the lowest activation barriers)? > > I wonder to know how can I set the parameters and in which condition I > obtain the structure by thermodynamics, and in which condition (with which > parameter setting) I can obtain the structure by kinetics. > > >> MD samples the free-energy surface. Its shape and the temperature > determine what structures might be found, and in what proportions. > > Do you mean that I can obtain the structure by thermodynamics in longer and > higher temperature ; obtain the structure by kinetics in shorter and lower > temperature? > > > You are drawing some artificial distinction whose purpose I do not > understand. A short simulation on a FES at a temperature low enough that > the barriers are larger than the readily available KE will be kinetically > trapped. I'd guess that most MD simulations that have ever been run have > suffered from this defect. The shape of the FES will generally vary with > temperature also. > > Mark > > > > > > 2011/9/26 Mark Abraham <mark.abra...@anu.edu.au> > >> On 26/09/2011 6:41 AM, xiaojing gong wrote: >> >>> Dear all, >>> A question about, in MD, in which situation you can obtain a structure >>> with lowest energy. >>> >> >> Any dynamical simulation has a lowest-energy structure... whether this >> means anything is another question. >> >> >> Can MD simulate the kinetics process, and obtain a stuctrue with the >>> lowest activation barriers? >>> >> >> Mapping free-energy surfaces where bonds are not made or broken can be >> done with conventional MD. >> >> >> Typically, are the structures we find with MD determined mainly by >>> thermodynamics or by kinetics ? >>> >> >> MD samples the free-energy surface. Its shape and the temperature >> determine what structures might be found, and in what proportions. >> >> Mark >> -- >> 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 >> > > > > > > -- > 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 >
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